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Skyline 24.1 Released

Wed Jul 17 14:38:47 PDT 2024

Dear Skyline Users, The Skyline Team is excited to release Skyline 24.1, the product of another 10 months of effort in response to your feedback and use of Skyline. Since our last release, you have started 15,000 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1600 times per month. There have been 1291 posts to the support board. Improvements in Skyline 24.1 include: - **New!** File > Search submenu putting all our search pipeline options in a place you can find. - **New!** Complete support for FragPipe and DIA-NN integration. - **New!** Complete EncyclopeDIA pipeline with narrow and wide window searches and staggered window demultiplexing. - **New!** File > Import > Features Detection - MS1 peptide feature finding with Hardklor/Bulseye. - **New!** MS/MS spectrum and RT prediction with Koina (Prosit model available). - **New!** Peak Areas > Relative Abundance plot. - Added right-click Auto Arrange Labels option on the Group Comparison - Volcano and Peak Areas - Relative Abundance plots for publishable figures. - Added matching small molecule versions of all standard peptide reports in Document Grid. - Added gene level parsimony option in protein association dialog. - Added File > Open from Panorama with anonymous account access to Panorama, e.g. Panorama Public. - Added "Peptide Spectrum Match Count" to the PeptideResult in the Document Grid. - Added support for Proteome Discoverer 3.1 in spectral library builder. - Added modification and special fragment ions for TMTpro. - Added support for precursor isotopes and reporter ions to transition list import. - Added support in Spectral Library Explorer for contains search by using preceding asterisk, e.g. *IDE. - Added tooltips to the Peak Areas - Replicate Comparison plot. - Added command-line arguments for File > Export > Spectral Library. - Added command-line arguments for File > Export > mProphet Features. - Added command-line arguments for peptide digestion settings. - Added command-line arguments for peptide filter settings. - Added command-line arguments for File > Export > Annotations. - Added command-line argument --import-pep-list. - Added command-line argument --associate-proteins-fasta for associating existing document peptides with a FASTA. - Added command-line arguments --pep-add-mod*, --pep-clear-mods, and --integrate-all. - Added command-line argument —pep-add-mod-variable= for explicit setting of peptide modifications to “variable” or “fixed”. - Added command-line arguments to add annotations. - Added command-line argument --verbose-errors to help troubleshoot unexpected errors. - Added support for reading chemical formulas with Unicode numeric subscript text. - Added "Surrogate External Standard" that can be set on Peptides and Molecules in the Document Grid which enable using a different molecule's calibration curve for quantification. - Added ion mobility columns for library building SSL format. - Added support for Agilent MassHunter 12 method export. - Added support for Thermo Astral and Orbitrap GC instruments. - Added method export support for the Thermo Stellar instrument. - Added support for SCIEX OS software (exporting acquisition methods and quantitation methods) for QQQ/QTRAP and QTOF platforms. - Added support to treat WIFF1 and WIFF2 as separate types (e.g. for purposes of import results form) - Added File > Export > Transition List for Agilent MH 12.1. - Added Dot Product value to Full-Scan view property grid that compares the spectrum in the plot with the expected distribution. - Added "Replicate Name" to the things that can be set using Result File Rules. - Added warning to the immediate window when a CCS<=>IM conversion fails. - Added warning when adding decoys or training an mProphet model if document uses explicit peak boundaries from spectral libraries. - Added red text and warning tooltip on Transition Settings - Full Scan tab if retention time filtering is selected with "PRM" or "SureQuant" acquisition methods. - Added isotope distribution matching to pick best ion mobility value in ion mobility library "Use Results". - Added support for MSFragger pepXML/mzML pairs for Bruker timsTOF data with plain integer scan numbers in the spectrumNativeID attribute. - Update to MassLynxSDK 4.11.0. - Updated Shimadzu data reader DLLs. - Updated SCIEX method export DLLs. - Updated to MSFragger 3.8. - Updated available modifications to current UniMod, Mascot naming, and ProteinPilot abbreviations. - Improved peak quality indicators in the Targets view for the colorblind. - Improved performance of .sky file reading. - Improved performance of "Aligning Retention Times". - Improved performance displaying protein tooltips (and Library Match window) when Max Neutral Losses is high. - Improved CE Optimization method and transition list export for Agilent to stop adding 0.01 to the Q3 m/z values. - Improved Associate Proteins form to keep unmapped peptides in an "Unmapped Peptides" list, and hide min peptides per protein option when called from the Refine menu. - Improved sort order for adducts so that molecule precursor ions are ordered by mass, as with peptides. - Improved "Apply Peak" to work with multiple-selection in the Targets tree. - Improved Spectral Library Explorer to suggest adding "common" modifications instead of less common modifications when unknown modifications are found in library. - Improved Spectral Library Explorer for a better experience with larger small molecule libraries. - Improved error handling when attempting to parse formulas with errors in mass offsets, e.g. "C12H5H3[+3.2/3x3]" - Improved TMT support by excluding reporter ions when calculating library dot products and detecting peaks. - Improved tolerance for ion mobility data with bad CCS calibrations. - Improved error message display interacting with Panorama. - Improved peptide Unimod modification defaults for "variable" and "fixed" to make only alkylation, isobaric tag labels, and loss-only modifications "fixed" by default. - Expanded DIA isolation scheme detection to 1000 spectra cycles for gas phase fractionation (GPF) and Astral. - Reduced the minimum number of values required for a dot product to be calculated from 3 to 2. - Changed so that the "Do you want to add decoys" message only gets shown for DIA when importing results if the document has at least 20 peptides in it. - Changed to reset standards in File > New to decrease confusion over documents with unexpected "light" as standard instead of "heavy". - Changed values such as "Normalized Area", "Calculated Concentration" to have a value even when some peaks are missing or truncated. - Warning messages are displayed in Document Grid. - Old behavior is available with "Normalized Area Strict" sub-property in Document Grid. - Fixed error that sometimes happens choosing "Kernel Density Estimation" on Retention Times run to run regression graph. - Fixed error that could happen when clicking on an ID line on the chromatogram graph. - Fixed calculation of bogus isolation window offsets when WIFF2 file returns 0 for lower/upper window bounds. - Fixed Associate Proteins form to use final document counts for proteins and peptides in the "prot, pep, prec, tran" string (so it includes decoys, iRT, and the unmapped peptide group in the count). - Fixed MSAmanda to write PeptideEvidence with isDecoy attribute. - Fixed IdentData mzIdentML parser to be case-insensitive on isDecoy attribute. - Fixed case where View > Transitions > QC shows blank menu item instead of list of available QC graphs. - Fixed Import Transition List / Assay Library to allow users to deal with errors after click on OK if errors were previously reviewed. - Fixed "Chromatogram Information Unavailable" in small molecule document with spectrum filters. - Fixed centroiding for Waters non-IMS data to be done spectrum by spectrum instead of all at once. - Fixed repeated neutral loss labels on crosslinked peptide transitions in Library Match view. - Fixed unexpected error copying and pasting protein groups. - Fixed unexpected error hovering over Protein in Targets tree if .skyd file cannot be read. - Fixed incorrect TIC area in documents with QC traces and transition full scan retention time filtering. - Fixed unexpected error in small molecule transition list reader. - Fixed edge case in detection of Waters lock mass channel. - Fixed "times and intensities disagree in point count" error applying a Spectrum Filter to an MS1 Transition. - Fixed reading compensation voltage values from mzML files. - Fixed unexpected error extracting chromatograms from raw file when there are pressure traces but no MS1 spectra. - Fixed command-line output of transition full-scan settings changes. - Fixed unexpected error attempting to modify base molecule in targets tree with an invalid chemical formula. - Fixed WIFF SIM/SRM chromatogram extraction to operate on the entire time range instead of within the scheduled limits. - Works around a bug(?) with Sciex WIFF where it records the wrong scheduled limits but the data is there if you tell it to ignore the limits. - Fixed Bruker TSF reader crashing when enumerating chromatograms when the file has empty spectra. - Fixed library build from pepXML to check for spectrum files in the base_name's parent path (if present). - Fixed small molecule chromatogram extraction to limit time range based on retention time prediction. - Fixed to update Document Grid when annotations are removed from the document. - Fixed DIA-NN speclib N-terminus mods to be moved/merged to the N-terminal AA. - Fixed spurious Skyline Batch error about empty directory when directory contained .d folders. - Fixed error displaying dot product line on Peak Area Replicate Comparison graph when currently selected peptide has no transitions of the type (precursor or product). - Changed to display a warning message in the Immediate Window when Skyline discards chromatograms because the Explicit Retention Time is outside the retention time range over which the chromatogram was extracted. - Fixed BiblioSpec to use the spectrumNativeID attribute in pepXML when reading MSFragger pepXML. - Fixed unexpected error ("Attempt to add integration information for missing file") when doing a rescore with multiple injections if it fails because of missing iRT standards. - Fixed transitions getting incorrectly added/removed from siblings when changing children of a precursor with a Spectrum Filter. - Fixed unexpected error in Edit Spectrum Filter form. - Fixed unexpected error when selected QC trace is not present in a particular replicate. - Fixed truncation of report text copied to the clipboard when report columns include "CleavageAa". - Fixed command-line arguments --tran-product-*-special-ion not being processed if they are the only filter arguments passed. - Fixed Skyline detection of Waters RAW folders to be case-insensitive. - Fixed error that could happen if DIA-NN chosen peak was outside of extracted chromatogram range. - Fixed unexpected error in Retention Times Replicate Comparison graph when aligning retention times and there are missing results. - Fixed unexpected error in the Detections plot. - Fixed unexpected error importing peak boundaries with malformed peptide modification. - Fixed unexpected error when spectrum from an extracted chromatogram cannot be found in the raw file. - Fixed incorrect isotope dot product for newly imported small molecule precursor transition. - Fixed MS1 chromatogram extraction when doing PRM CE Optimization. - Fixed adducts like [M+H-H2O] on molecules described as mass-only. - Fixed unexpected error in Peak Areas > Replicate Comparison graph when a peptide has missing results for one replicate. - Fixed unexpected error bringing up Full-Scan spectrum view on some datasets. - Fixed unexpected error displaying TIC chromatogram when not available in some datasets. - Fixed parsing spectrum IDs from MSFragger pepXML files with MGF spectrum files. - Fixed unresponsive long wait when doing "Equalize Medians" in huge documents. - Fixed unexpected error using "Apply Peak to All" when one replicate has missing chromatograms. - Fixed unexpected error importing a small molecule transition list. - Fixed unexpected error after Modify Molecule form to change charge state in a way that makes no sense with the current adduct. - Fixed unexpected error after Modify Transition form to change the precursor adduct in a way that makes no sense with parent molecule, or vice versa. - Fixed unexpected error exporting a report definition to a .skyr file that cannot be written to. - Fixed to output a warning message to the Immediate Window if a single transition's chromatogram is being discarded because of the Explicit Retention Time. - Fixed unexpected error using "Edit Modifications" form. - Fixed volcano plot formatting when Match Expression includes both fold change and p-value. - Fixed loss annotations in MS/MS spectra to work for mass-only losses. - Fixed unexpected error in Spectral Library Explorer when amino acid 'J' had a modification on it. - Fixed unexpected error showing Detections graph when document has no results. - Fixed preventing multiple spectrum filters from being added to heavy precursor. - Fixed optimization step incorrect for some Agilent collision optimization data. - Fixed "Matrix must be positive definite" error that sometimes happened with bilinear fit calibration curves. - Fixed handling explicit adduct charge declarations (e.g. the trailing "+" in "[M+2CH3+Cl]+"). - Fixed Panorama error "Documents with same GUID should have same first audit log entry" when audit log restarted. - Fixed unexpected error showing full scan graph when transitions differ only be neutral loss. - Fixed unexpected error doing "Apply Peak to All" when retention times have been aligned. - Fixed unexpected error searching for missing peak scores when peptide is missing results for one replicate. - Fixed chromatogram weirdness when renamed molecule used to have the same name as another molecule in the document. - Fixed disk error that would sometimes happen at end of chromatogram extraction. - Fixed Edit > Find (Ctrl-F) form to set focus to the text box for immediate typing. - Fixed several command-line operations that were not being recorded in the Audit Log. - Including "--import-annotations", "--import-peak-boundaries", "--reintegrate", "--add-decoys", and "--import-file". - Fixed graphs sometimes blank when displaying more than 100 precursors at the same time. - Fixed error adding decoys to a document with high resolution MS1 and sulfur containing amino acids. - Fixed exporting negative RT values in Agilent instrument methods. - Fixed using too much memory outputting report with "Normalized Area" column when document has Peptide Quantification regression method set to something other than "None". - Fixed reading CE from WIFF file spectra. - Fixed search errors from Search control to be more specific. - Fixed ion mobility values from spectral libraries (with no .imsdb file) not appearing in reports. - Fixed to gracefully handle network error during chromatogram loading. - Fixed potential hang extracting chromatograms when some protein groups have proteins with nonstandard accession numbers. This release will require a manual upgrade. We hope you'll take the time to visit the Skyline installation page: https://skyline.ms/skyline64.url And install this latest release. It should be worth the effort. Thanks for your continued use, feedback, and support of the Skyline Project. Brendan MacLean Skyline Principal Developer

PATCHED: Skyline 23.1 (380 - cf25ad847)

Mon Jan 15 18:11:23 PST 2024

Dear Skyline Users, I have just released a patch to Skyline 23.1 which contains the following improvements over the initial release: - Finalized Chinese and Japanese translation text. - Fixed File > Export > Method for Waters TQ instruments. - Fixed removal of useful reports in small molecule mode "Molecule RT Results" and "Molecule Transition Results". - Fixed error extracting chromatograms from raw file when there are pressure traces but no MS1 spectra. - Fixed incorrect TIC area in documents with QC traces and Transition Settings - Full-Scan retention time filtering. We think these improvements make Skyline 23.1 even better and hope you will update to this latest version soon. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

Skyline 23.1 Released

Sun Sep 24 21:10:14 PDT 2023

Dear Skyline Users, The Skyline Team is excited to release Skyline 23.1, the product of another 12 months of effort in response to your feedback and use of Skyline. Since our last release, you have started 13,000 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1200 times per month. There have been 1675 posts to the support board. Improvements in Skyline 23.1 include: - **New!** [EncyclopeDIA search](https://skyline.ms/wiki/home/software/Skyline/page.view?name=EncyclopeDiaSearch) support in File > Import > Peptide Search for DIA data. - **New!** [Spectrum filters](https://skyline.ms/wiki/home/software/Skyline/page.view?name=SpectrumFilters) for extracting separate chromatograms for precursors handled differently in the mass spec e.g. different detectors or fragmentation methods. - **New!** Parameter (CE) optimization for TOF and Orbitrap instruments. - Added spectrum properties to Library Match view. - Added spectrum properties in the Full-Scan graph. - Added annotations for "Special Ions" (e.g. TMT) in MS/MS graphs. - Added library ion match tolerance unit setting in the transition settings to support PPM values. - Added "ChromatogramStartTime" and "ChromatogramEndTime" to Transition Result Chromatogram in Document Grid. - Added Skewness, Kurtosis, Standard Deviation, and Shape Similarity Score to Transition Results in Document Grid. - Added new command-line arguments for building ion mobility libraries: --ionmobility-create-library and --ionmobility-create-library-name - Bruker PaSER support improvements: - Recognize "PrecursorIonMobility" as a synonym for "1/K0". - Store ion mobility values from File > Import > Assay library in the .blib file. - Added library build support for Bruker Paser results and library. - Added library build support for crosslinked peptide sequences in .ssl files. - Added library build support for PeptideProphet .proxl.xml files. - Added library build support for MeroX proxl.xml files and cleavable crosslinks. - Added support for putting results files in File > Share .sky.zip. - Added support for showing a library match spectrum with multiple precursors selected. - Added tooltips on Libraries and Modifications lists in Peptide Settings dialog. - Added more choices when defining Group Comparisons. - Added support for Agilent DAD spectra and UIB chromatograms. - Added log output of the count of BiblioSpec PSMs that do not pass the score filter and improved error message when score filter is the cause of no PSMs being added. - Added support for File > Export > Method for Thermo Fusion Lumos and Eclipse. - Added support for File > Export > Method for SCIEX 7600. - Added pressure trace support for Thermo files. - Added an error in library builder when SSL peptide sequence has non-uppercase letters or unsupported modification formats. - Enabled setting the Standard Type of a peptide using "--import-annotations" command line argument - Added "Skyline 22.2" to the list of available formats in the "File > Share" dialog. - Added support for Proxl XML files from pLink. - Added a button to the toolbar in the View > Spectral Libraries form to show extended properties of the spectrum shown in the graph. - Added a button to the toolbar at top of Report Editor to toggle whether properties are sorted alphabetically. - Changed the find box on the Document Grid to start out case insensitive. - Changed right-click > Replicates > Best in the Targets view from being remembered between runs because it can be confusing. - Improved display display performance of Edit Modifications form. - Improved support for EncyclopeDIA .elib spectral library files. - Improved handling of small molecule transition lists where document settings can help with precursor isotopes. - Improved handling of .skyp files downloaded from Panorama to show progress and request log-in information. - Improved error handling when downloading MSGF+ fails. - Improved importing .MSP library files for GCMS use. - Improved default size of Audit Log, PCA Plot and HeatMap when they are first shown. - Improved support for interactive tools: - Added tool service method "ImportPeakBoundaries". - Improved performance of tool service method "DeleteElements". - Improved error reporting when communicating with Panorama. - Improved error reporting when unzipping an external tool. - Improved temp file cleanup and testing when running peptide search tools. - Improved error handling when parsing FASTA in Associate Proteins form. - Improved score information on Library Details form in View > Spectral Libraries. - Improved detection of lockmass function in Waters .raw files. - Updated to Bruker TDF-SDK v2.21. - Added Bruker TSF format support. - Update WIFF2 SDK to support all instruments. - Updated handling of Waters DDA data. - Updated Mascot Parser to 2.8.1 for parsing Mascot DAT files to build spectral libraries. - Increased limit on number of spectra that could be in a spectral library from 16 million to more than 100 million. - Fixed View > Transitions > QC showing blank menu item instead of the list of available QC graphs. - Fixed an unexpected error importing a small molecule transition list lacking anything like a "name" column. - Fixed library details for EncyclopeDIA .elib files. - Fixed MSFragger DDA search handle DDA PASEF data correctly. - Fixed errors caused by assuming lockmass function is not IMS: Invalid Scan Number exceptions. - Fixed "Order By" menu item disappearing when grouping peak area graph on a replicate annotation which no longer exists. - Fixed to allow changing score threshold when building library from Waters MSe final_fragment.csv files. - Fixed bug where half of all transitions in certain .elib files would be marked as non-quantitative. - Fixed blank panes in peak area peptide comparison when "Transitions > Split Graph" and "Scope > Protein" and selected protein has fewer label types than document. - Fixed library builder to read MaxQuant msms.txt files with UTF-8 byte order mark. - Fixed error when crosslinked peptides has heavy atoms. - Fixed PDF URLs in Start Page to tutorials updated for 22.2. - Fixed a number of proteomics features still showing up in small molecule UI mode. - Fixed CCS values to be recalculated as needed in chromatogram extractions for consistency in reports. - Fixed the Ion Mobility Library Editor to show friendly molecule names in (e.g. "Sulfamethizole" rather than "#$#Sulfamethizole$C9H10N4O2S2$") - Fixed Ion Mobility Library Editor to avoid absurd high energy offset values from "Find Results" - Fixed an unexpected error in peptide transition list import. - Fixed several cases where Skyline could produce a saved file that it could not open. - Fixed error when crosslinker attaches to invalid amino acid position. - Fixed calculation of m/z of cleavable crosslink fragments. - Fixed library build to read ion mobility vendor files in combined spectra form (addresses library build taking forever to try to read MSAmanda searches direct from ddaPASEF .d). - Fixed to preserve all decimal places of predicted retention times. - Fixed error doing "Save As" on document with very large .skyd file after removing a replicate. - Fixed error if SRM chromatogram has zero points in it. - Fixed hard crash when reading corrupt SQLite file in Bruker data. - Fixed issue where protein descriptions assigned by "Associate Proteins" would disappear when the document was saved and reloaded. - Fixed library builder reading newer MSFragger output from timsTOF. - Fixed MSFragger searches with C-terminal mods giving error "'c' is not an amino acid". - Fixed a logic flaw where Agilent GC-TOF EI data was mistaken for non-GC all ions data. - Fixed error clicking on transition with missing chromatogram when viewing single transition chromatogram. - Fixed converting Shimadzu DDA precursor m/z values from integers; 1e9 instead of 1e5. - Fixed audit logging for Import Peptide Search to stop logging a global cut-off score when the threshold is specified per file. - Fixed display of dockable window drop target when dropping near right edge of Skyline window. - Fixed location of dockable window drop targets when multiple screens have different screen resolution. - Fixed issue where changes to column values such as "Protein Note" made in the Fold Change grid seemed to disappear immediately. - Fixed cases where fold change value is NaN if measured peak area is zero. - Fixed unexpected error right-clicking in Library Match window. - Fixed unexpected error for protein group metadata during saving. - Fixed applying Result File Rules when importing results using the command line. - Fixed Chinese translation of "irank". - Fixed downloading MSGF+ Java virtual machine. - Fixed ion type menus in View > Spectral Libraries, Spectrum Match view, and Full-Scan view. - Fixed an unexpected error that could happen in Import Transition List if .skyd file is modified. - Fixed the way that the background level under the peak is shaded when TransformChrom is something other than Interpolated. - Fixed issue where document could not be loaded if a crosslinked peptide was added from the spectral library viewer but the crosslink modification did not have a checkmark next to it in peptide modifications settings. - Fixed behavior of missing peaks for spectral libraries with peak boundaries (e.g. DIA-NN, EncyclopeDIA, OpenSWATH). - Fixed error handling in grids appearing in Settings forms. - Fixed unexpected error on MIDAS library load failure. - Fixed MIDAS library support in View > Spectral Libraries. - Fixed unexpected error in spectrum Full-Scan view. - Fixed handling chemical formulas with zero-count declared atoms. - Fixed issues with DIA-NN speclib parsing in library builder. - Fixed Spectral Library Explorer source files view to more consistently report statistics. - Fixed handling of user editing a molecule in ways that make no sense with child precursor adducts. - Fixed issue with mirror spectrum between multiple libraries in Library Match view. - Fixed issue where "--report-add" commandline argument would cause all reports from "External Tools" group to be copied to the "Main" group. - Fixed chromatogram extraction with ion mobility filtering to use high energy IM offset values for all MS/MS acquisition modes rather than only "All Ions". - Fixed issue where Library Match graph disappears if spectrum being displayed has no intensities that are greater than zero. - Fixed unexpected error using Prosit when precursor charge was greater than 6. - Fixed assay library importing to handle unsorted transition lists. - Fixed toolbar buttons and right-click menu in View > Spetral Libraries broken adding property page. - Fixed very large (e.g. 6 million lines) Assay Library import. - Fixed out-of-memory error. - Fixed performance bottleneck introduced in checking for lines with irregulate column counts before starting to import. - Fixed requiring large recalculation when "Check For Errors" was already clicked. - Fixed "The document specific spectral library does not have valid retention times" when importing peptide search existing EncyclopeDIA 2.0 library. - Fixed a problem with Agilent IMS data where fringe CCS and/or DT values cannot roundtrip through the CCS/DT conversion. - Fixed a case where saving document after removing modification with neutral losses from settings results in a document which cannot be opened. - Fixed a case where ion mobility library entries for crosslinked peptides would be duplicated each time you pressed the "Use Results" button . - Fixed peptide losses with multiple charge states not all appearing in the transition options. - Fixed peptide charged losses changing to small molecule adducts line [M+H]. - Fixed Result File Rule Set Editor to allow using newly added annotations without having to first OK the Document Settings dialog. - Fixed Document Grid (and other data grids) so that custom formats are applied when doing "Copy All" or "Export". - Fixed unexpected error changing annotation value in document grid when the document had been changed. - Fixed issue where removing an explicit modification from a document with decoys could result in a document that could no longer be opened. - Fixed exporting Waters methods containing compounds with multiple modifications and more than 5 transitions. - Fixed behavior where graphs would appear blank if the Legend took up all of the space in the graph. - Fixed several issues with Bruker data: - Fixed timsTOF instrument type not being recorded in instrumentConfiguration. - Fixed negative CE in negative polarity Bruker data not being reported. This release will require a manual upgrade. We hope you'll take the time to visit the Skyline installation page: https://skyline.ms/skyline64.url And install this latest release. It should be worth the effort. Thanks for your continued use, feedback, and support of the Skyline Project. Brendan MacLean Skyline Principal Developer

IMPORTANT: Upgrade Skyline 22.2 to the Latest Patch (22.2.0.527)

Mon Jun 12 16:14:40 PDT 2023

Deat Skyline Users, If you are using Skyline 22.2 please **UPGRADE NOW!!** To the latest patch release Skyline 22.2.0.527. If you are not using Skyline 22.2 or you fail to make this upgrade before our next major release, you will need to use our recovery instructions for your next upgrade: https://skyline.ms/install_recover.url We were forced to change our code signing key this year for the first time in 15 years. If you make this upgrade successfully, you shouldn't notice. We have already started using it without complaints on our Skyline-daily release. Also in this patch, you will get the following fixes: - Fixed URLs for the Tutorials tab in the Start Page. - Fixed a bug where protein descriptions assigned by "Associate Proteins" would disappear when the document was saved and reloaded. Thanks for making this upgrade a priority. --Brendan

UPGRADE !! To Skyline 22.2

Thu May 11 19:48:32 PDT 2023

Dear Skyline Users, Nearly 90% of start-ups are currently Skyline 22.2 or Skyline-daily. If you are not yet, please **UPGRADE NOW**. Soon, I will make the last patch release to Skyline 22.2 and if you do not: 1. **UPGRADE NOW** to the latest 22.2.0.255 2. Upgrade to the patch when it is announced You will stop being able to receive automatic updates when we release Skyline 23.1 and will likely need to follow our instructions on recovering from a broken installation to get that ability back: https://skyline.ms/install_recover.url This was unavoidable. After 14 years of maintaining a continuous line of code-signing keys we were forced into an update that causes this issue. Hopefully, it will be another 14+ years before this happens again. Thanks for upgrading to our latest. It really is our best. --Brendan

PATCHED: Skyline 22.2 (351 - 28f9b9301)

Mon Dec 19 10:33:35 PST 2022

Dear Skyline Users, I have just released a patch to Skyline 22.2 which contains the following improvements over the initial release: - Finalized Japanese translation text - Fixed downloading MSGF+ Java virtual machine Upgrade NOW! We hope you will take this opportunity to upgrade to Skyline 22.2 as this may be the final patch before 23.1. Don't miss out on all the improvements we made in 22.2. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

PATCHED: Skyline 22.2 (312 - 7f626e76d)

Tue Nov 08 15:41:12 PST 2022

Dear Skyline Users, I have just released a patch to Skyline 22.2 which contains the following improvements over the initial release: - Finalized Chinese translation text - Fixed an unexpected error with mirror spectrum in the Library Match view - Fix issues with library building for DIA-NN .speclib files where not all runs were included - Fixed synchronized integration with missing or removed peaks not working - Fixed performance problem with manually integrated peaks with many transitions - Fixed checking for Bruker timsTOF ion mobility issues before showing method scheduling graph - Fixed an unexpected error getting metadata for protein groups - Fixed NaN's that appear in fold change values in PRM Orbitrap tutorial using Tukey's Median Polish - Fixed dotp highlighting (red dots) in Peak Areas - Replicate Comparison plots to appear in front of peak area bars - Fixed admin installer for SCIEX OS method export We think these improvements make Skyline 22.2 even better and hope you will update to this latest version soon. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

Skyline 22.2 Released

Mon Sep 12 17:21:19 PDT 2022

Dear Skyline Users, The Skyline Team is excited to release Skyline 22.2, the product of another 8 months of effort in response to your feedback and use of Skyline. Over the past 8 months, you have started 12,500 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1100 times per month. There have been 1000 posts to the support board. Improvements in Skyline 22.2 include: - **New!** Protein grouping - through File > Import > Peptide Search and Refine > Associate Proteins. - **New!** Library build interface that shows filter cut-offs in a grid, one per file with score type and appropriate scale, i.e. 0.01 for q values. - Improved DDA MS/MS peak integration to not use background subtraction, proven to work better for producing high dotp values. - Improved peak picking with DDA acquisition method to use "dotp" score when it is above 0.75, likely from a high-quality MS/MS acquired within or near the MS1 peak. - Added support for ignoring SIM spectra (commonly used by Thermo as a diagnostic) in MS1 chromatogram extraction. - Added support for z+1 and z+2 ions for EAD/ETD MS/MS fragmentation. - Peak Areas plot r/i/dotp line graph support made the default, with customizable cut-off highlighting. - Added Candidate Peaks view - for new visibility into how Skyline scores and chooses among peaks. - Added small molecule support to File > Import > Peak Boundaries. - Recognizes a "molecule" or "molecule name" column - analogous to the existing "peptide" column for proteomics documents - Added a new standard report "Small Molecule Peak Boundaries" for exporting peak boundaries for small molecule documents. - Added "--import-peak-boundaries" command-line argument. - Added File > Export > Isolation List support for Bruker timsTOF. - Added support for redundant iRT databases. - Added an option to minimize libraries included with a Skyline document uploaded to Panorama. - Added a context menu option to show collision energy in Full-Scan graph. - Added method export support for SCIEX 7500. - Added “natural sort” algorithm to the file explorer and document grid. - Support for Ion mobility values added for peptide-oriented transition list and assay library imports. - Improved default peak scoring model training to allow features that have some unknown score values to be used. - Improved error reporting when importing small molecule transition lists. - Improved keyboard support for undo (Ctrl-Z) and redo (Ctrl-Y) and fill-down (Ctrl-D) within a floating Document Grid. - Improved UI of new Edit > Insert > Transition List form with bigger text instruction in the middle of the form. - Improved error handling for exporting SCIEX method. - Improved memory consumption in Document Grid when a large amount of Peptide Normalized Area values are being calculated. - Improved spectrum annotation to allow show/hide of neutral losses. - Added "[M+]" and "[M-]" to the cascading dropdown control for composing ion formulas in the "Modify..." right-click menu item in the Targets tree for small molecules. These were already available for fragment ions but they are also useful for precursors. - Added support for heavy copper (Cu' in Skyline formula syntax, Cu65 in adduct syntax) - Made peptide transition list import "Associate Proteins" option enabled by default when a background proteome is available. - Fixed the Administrator Installer to avoid causing Windows to show a warning before running it. - Fixed "Array dimensions exceeded support range" error that can happen when extracting chromatograms from a file with no MS1 spectra. - Fixed error opening a new Skyline document while there was an uncommitted change in a text box in the Document Grid. - Fixed unexpected error updating an external tool. - Fixed reading mzXML from mzML parentFile. - Fixed mzXML parser to treat invalid scanType attributes (e.g. "CID") as full scan MS1/MSn with a warning. - Fixed library builder pepXML reader to skip non-AA characters in the unmodified peptide sequence. - Fixed sticky Y axis in the Full-Scan view. - Fixed mode-specific (proteomics vs. molecule) reports to show/hide based on the mode and added molecule-specific reports for quantification. - Fixed some inconsistent handling of attempts to add an empty transition list. - Fixed a problem with reading transition lists defined by m/z only, and with implied isotope labels. - Sped up generating the list of peptides with missing values from the edit peak scoring form. - Fixed chromatogram display when optimization data is asymmetric as when CE values go to zero and below. - Fixed FASTA parser unexpected error when faced with unusual header lines. - Fixed NullReferenceException that can happen when extracting chromatograms and predicted retention times are outside of range of spectra. - Fixed problem where, when doing "File > Share > Minimal", peptides in the document which had modifications would not end up in the minimized iRT database. - Fixed the display of peak boundaries on the chromatogram graph when all transitions shown are non-quantitative as in DDA. - Fixed inappropriate use of MS/MS in peak picking scores for DDA acquisition method. - Fixed unexpected error in Library Match view. - Fixed unexpected error that can happen showing the PCA plot if the dataset has only one numeric column. - Fixed unexpected error doing "Apply Peak" when one result file in a replicate was missing results. - Fixed unexpected error using too long of a path when doing "Save As". - Fixed Divide by Zero error minimizing a document that has replicates but no chromatograms. - Fixed error in full scan spectrum viewer that could happen if you rapidly click multiple times on the chromatogram graph. - Fixed TIC for WIFF files. - Fixed SkylineDailyRunner.exe to work with Windows user names that contain ampersand (&) or caret (^). - Fixed synchronized integration behavior when acting on a chromatogram not selected for synchronization. - Fixed error trying to use small molecule spectral library which did not contain chemical formulas. - Fixed localization of "Ratio to Global Standards" etc. label on the Y-axis of peak area graph. - Fixed issues building spectral libraries from Proteome Discoverer files. - Fixed error that could happen if a particular precursor did not have any results. - Fixed issue determining score type for .mzid files. - Fixed error that can happen in small molecule documents if you remove an isotope label type that is still being used by some of the precursors in the document. - Fixed a problem with Fixed Width ion mobility window value not saving properly when changed in Settings>Transition Settings>Ion Mobility. - Fixed error displaying multiple peptide chromatogram graph if any of the chosen peaks has a start retention time equal to zero. - Fixed to not calculate Protein Abundance on the decoy peptide list since it is sometimes very slow. - Fixed problem with downloading tools that have invalid URL characters in their identifiers. - Fixed unhandled error when inserting crosslinked peptide sequence which specified "0" as amino acid position. - Fixed unhandled error inserting crosslinked peptide whose precursor m/z was very close to Instrument Max Mz setting. - Fixed problem where opening a document with a background proteome and a peptide uniqueness constraint sometimes results in all peptides being removed from document. - Fixed ion mobility libraries for crosslinked peptides. - Fixed problem where Skyline would allow transitions which contained multiple crosslink fragment ions which were not actually attached to each other. - Fixed log scale y-axis label not showing median normalization when appropriate. - Fixed audit logging in Import Peptide Search wizard when an existing library is used. - Fixed case where Full-Scan settings impacted peak picking in SRM data. - Fixed incorrect display of median and TIC normalized values in Peak Area graph. - Fixed incorrect calculation of median and TIC normalized areas and group comparisons in some replicates. - Fixed problem where Protein Abundance could not be displayed in a report unless the report also included columns from Peptides. - Added new document grid columns "Median Peak Area" and "Normalization Divisor" in order to make it easier to see how Skyline calculates normalized areas. - Fixed calculating of Median Peak Area in the presence of reference standard peptides so that it uses only internal standard label type peak areas. - Fixed spectrum from incorrect file from EncyclopeDIA library displayed in Library Match window. - Fixed unhandled error when trying to paste into the Document Grid when it is empty. - Fixed mass error sometimes reported as zero when "Triggered chromatogram acquisition" was checked. - Fixed DIA-Umpire on spectra that aren't sorted by m/z (e.g. from scanSumming timsTOF data) - Fixed a problem with FAIMS on MS2 data in Thermo SureQuant, resulting in jagged chromatograms. - Fixed support for building spectral libraries from ProxlXML files from Byonic (converted from mzIdentML). - Fixed unexpected error when exporting Bruker timsTOF methods with ion mobilities outside template range. This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page: https://skyline.ms/skyline64.url And install this latest release. It should be worth the effort. Thanks for your continued use, feedback, and support of the Skyline Project. Brendan MacLean Skyline Principal Developer

PATCHED: Skyline 21.2 (565 - 17c47d8e1)

Wed Jul 20 21:32:35 PDT 2022

Dear Skyline Users, We just couldn't resist one last patch to Skyline 21.2 which contains the following improvements over the last patch release: - Fixed scheduling graphs showing concurrent precursors when labeled concurrent transitions. - Fixed an unexpected error parsing unrecognized FASTA header lines. - Fixed communication with UniProt for protein metadata. - Fixed small molecule transition list import to issue a warning in some cases where it caused unexpected errors. We hope you enjoy using this patch. Next major release coming soon. --Brendan

PATCHED: Skyline 21.2 (536 - dbaf6ccd2)

Wed Jun 22 21:11:41 PDT 2022

Dear Skyline Users, I have just released a patch to Skyline 21.2 which contains the following improvements over the last patch release: - Fixed downloading MS Fragger due to a recent change to the release website. - Fixed error about missing "OFX.Core.Contracts.dll" when importing SCIEX 6500 QQQ wiff file. - Fixed problem where if the Targets tree was not supposed to be showing ratios, it would display raw peak areas followed by the word "ratio". Skyline should ask you to update the next time you restart or use Help > Check for Updates. We hope you enjoy using this patch. --Brendan

PATCHED: Skyline 21.2 (425 - e653b4c5e)

Tue Mar 01 12:27:18 PST 2022

Dear Skyline Users, I have just released a patch to Skyline 21.2 which contains the following improvements over the initial release: - Finalized Chinese and Japanese translation text - Fixed chromatogram display when optimization data is asymmetric as when CE values go to zero and below. - Fixed peptide settings to update normalization methods based on changes to heavy modifications. - Fixed ratios displayed in the Targets view. - Fixed Edit > Insert > Transition List character limit on pasted clipboard text. - Fixed library reading getting handled as unexpected errors rather than reporting them directly with a message. - Fixed a problem reading a transition list where, for example, C2H6N[M+H] and C2H6N[M2C13-H] were incorrectly treated as an m/z ambiguity. - Fixed a problem reading small molecule transition lists with isotope labels declared in precursor and fragment formulas with integer-only charge declarations. - Fixed a problem with reading transition lists defined by m/z only, and with implied isotope labels. - Fixed a problem handling transition lists with missing product m/z information. - Fixed a problem importing transition lists with an inconsistent number of fields per line. - Fixed Sciex method export issue and improved error reporting. - Fixed error that can happen moving the mouse across volcano plot after volcano plot has been docked and undocked several times. We think these improvements make Skyline 21.2 even better and hope you will update to this latest version soon. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

Skyline 21.2 Released

Tue Jan 04 16:05:41 PST 2022

Dear Skyline Users, The Skyline Team is excited to release Skyline 21.2, the product of another 7 months of effort in response to your feedback and use of Skyline. Over the past 7 months, you have started 11,000 instances each week (on average) of Skyline or Skyline-daily, and downloaded the software 1450 times per month. There have been 1100 posts to the support board. Improvements in Skyline 21.2 include: - **New!** Synchronized Integration (right-click in a chromatogram graph) - **New!** Improved SureQuant support with "SureQuant" MS/MS acquisition method and method export for Exploris. - Also added new PRM acquisition method (an improvement over the old "Targeted" method – now deprecated). - **New!** Added support for DDA searches with MS Fragger and MSGF+, now options in the Import Peptide Search wizard. - See the [DDA Search tutorial](https://skyline.ms/tutorial_dda_search.url) for more information on integrated DDA searches in Skyline. - Prompt to create decoys for DIA data and when decoys are present auto-train a default model to add q values and z scores. - Improved memory use for large-scale DIA to use less than half the memory in most cases. - Improved DIA-Umpire performance in Skyline. - Added support for transition list import with column selection form for small molecules. - Improved transition list column selection form to support Associate Proteins. - Replaced Edit > Insert > Transition List with for pasting text followed by the transition list column selection form to be consistent with direct pasting and File > Import Transition List. - Line graph representation of dotp/idotp/rdotp in the Peak Areas > Replicate Comparison plot - using right-click menu. - Changed rdotp calculation to be consistent with dotp and idotp - using spectrum contrast angle. - This will tend to reduce rdotp values slightly if comparing rdotp values after this change with those before it. - Added RT annotation display digits on the chromatogram graph right-click > Properties form. - Improve library building error message for unrecognized modifications in PLGS outputs to include the ones we will recognize. - Improved layout of Import Peptide Search wizard forms when ion mobility values are present, e.g. diaPASEF - Improved Export > Spectral Library to use best score instead of first and include z-score. - Improved library building support for MSFragger. - Improved performance importing large .MSP spectral library files. - Added ability to switch between centroided and profile spectra in Full-Scan view. - Added mass error annotation display to Full-Scan and Spectrum Match views. - Added rdotp annotation in Peak Areas > Replicate Comparison view when showing ratios. - Added new filter categories to the Spectral Library Explorer, especially helpful for small molecules. - Added support for reading from vendor formats when library build searches for spectra for pepXML ids. - Switched to using peptide level q values in pdResult files and special handling for 1% and 5% FDR cutoffs to be more consistent with Spectronaut library builds. - Added support for previously unseen "VIP_HESI" ion source in Bruker TIMS data. - Added support for the latest chromatogram library export from Panorama, including new support for ion mobility and small molecules. - Improved menu options for MS/MS annotations in the Full-Scan view. - Skyline no longer requires .NET 3.5. - Only write top-ranked transitions when exporting any CoV optimization method - Added a warning when exporting a prmPASEF method for timsTOF with wrong CE setting. - Export polarity column for Thermo Fusion when Tune v3 is checked. - Enabled writing CoV values for Thermo Fusion. - Improved support for Waters SONAR data. - Updated SCIEX interop DLLs for method export. - Update Shimadzu DLLs for method export. - Added support for Agilent/Mobilion SLIM data. - Added LC/QC chromatograms for Agilent data. - Added tooltips on feature names in mProphet model form. - Fixed peak scoring for documents using DDA acquisition method in Transition Settings - Full-Scan tab for MS/MS filtering. - Fixed Skyline to report AA positions in proteins starting at 1 instead of zero. - Added the columns "First Position" and "Last Position" to the document grid which show the 1-based amino acid position of the peptide in the protein. - Changed the numbers that are displayed in the Targets tree so that they are 1-based instead of 0-based. - Columns "Begin Pos" and "End Pos" are now marked "Obsolete", which means that they only show up in the Report Editor if you push the "show all columns" button. - Fixed problem where peaks with integration boundaries that were chosen by the user did not get their areas recalculated when you do a reimport. - Fixed handling all-ions DIA for Bruker timsTOF bbCID. - Fixed a problem reading Bruker files with multiple TIMS calibrations. - Fixed library building from DIA-NN speclib to support version 3, and added support for reading scores and ion mobilities. - Fixed peptide-specific settings showing up in the Transition Settings - Library tab when in small molecule mode. - Fixed MSAmanda running on DDA WIFF files. - Fixed handling unexpected errors during auto-training of an mProphet model. - Fixed case where "Ratio To" menu item in Targets view did not agree with "Normalize To" in Peak Areas view. - Fixed problem removing a Prosit library for library matching in Molecule UI. - Fixed unexpected error in heat map graph during a selection change. - Fixed Agilent method export for scheduled methods - Fixed an issue where a mass-only transition list import of a labeled precursor would come up with the unlabeled mass for the precursor transition. - Fixed "Missing transition precursors when you do Refine > Permute Isotope Labels". - Fixed "Item with the same key already added" when two small molecules have no Name, same precursor m/z and different set of transitions. - Fixed an unexpected error when attempting to parse an ill-formed adduct description. - Fixed InvalidOperationException choosing "Transform > None" when the displayed chromatogram has optimization steps. - Fixed loading libraries from read-only drive location. - Fixed problem where blank document created from the Start Page sometimes never loads. - Fixed unexpected error in Import Peptide Search when importing multiple results files with the same name. - Fixed preserving scores when using File > Export > Spectral Library. - Fixed command-line documentation to use tags instead of non-breaking hyphen for easier copy-paste. - Fixed transition list logic to decide proteomic vs. small molecule based on UI mode when no other indicators work. - Fixed right-click > Copy in any graph to show a useful error message if the clipboard is locked by another application. - Fixed error that happens if you set Instrument Min Time, but leave Instrument Max Time blank. - Fixed a problem where if "Triggered Acquisition" was chosen on Transition Instrument Settings, the reported peak areas would all be 60 times smaller than they should be (but did not impact light:heavy ratios). - Fixed Spectral Library Explorer handling of peptide with modified 'X'. - Fixed a problem where "Protein Abundance" column would display as "column not found" if the report also had any peptide-level columns. - Fixed tolerance of Shimadzu .lcd files not containing TIC information. - Fixed how Skyline detects the difference between peptide and small molecule transition lists to be first based on finding a peptide sequence with a matching precursor m/z. - Fixed writing CE and DP to large Skyline documents for upload to Panorama. - Fixed coloring of peak annotations in MS/MS spectra for small molecules. - Fixed filtering of targets when building spectral libraries from existing BLIB files. - Fixed an infrequent potential race condition in the DIA-Umpire implementation. - Fixed transition list column picker saving column assignments only when they are valid. - Fixed a recently introduced problem where we were not identifying transition list columns as numeric if the values were in quotes. - Fixed MaxQuant spectral library build to check up to 4 levels above msms.txt for spectrum files and improved the error message when files are not found. - Fixed a problem processing Waters Cyclic IMS data, wherein the lockmass functions do not have IMS data. - Fixed order by m/z method export bug when multiple precursors have the same m/z. - Fixed cases where "View" was used in the UI instead of "Reports". - Fixed calculation of R-squared for calibration curves that use "Linear in Log Space" fit. - Fixed an unexpected error that can occur when "Transition Settings > Ion Mobility > Use spectral library values when present" is enabled. - Fixed View > Library Match y-axis was not updating correctly in response to changes in selection in the Targets view. - Fixed .skyd file corruption problem which could happen if there were more than 60 million candidate peaks. This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page: https://skyline.ms/skyline64.url And install this latest release. It should be worth the effort. Thanks for your continued use, feedback, and support of the Skyline Project. Brendan MacLean Skyline Principal Developer

PATCHED: Skyline 21.1 (278 - fe50e66f2)

Wed Oct 06 12:33:19 PDT 2021

Dear Skyline Users, I have just released a patch to Skyline 21.1 which took longer than usual in an effort to respond to confusion caused by our DIA tutorials and Import Peptide Search wizard discovered in working with the authors of a new DIA comparison paper (https://pubmed.ncbi.nlm.nih.gov/34472865/). Thanks to the authors for contacting us and helping us to understand the initial confusion. We think the result will benefit the entire Skyline community, and we encourage you to review this paper and the revised tutorials. This release contains the following improvements over the initial 21.1 release: - Finalized Chinese and Japanese translation text - Fixes to Import Peptide Search wizard for [DIA tutorial](https://skyline.ms/tutorial_dia.url) and [DIA/SWATH tutorial](https://skyline.ms/tutorial_dia_swath.url) updates. - Fixes for DIA-Umpire integration (various). - Fixed an unexpected error with Ion Mobility settings. - Fixed an unexpected error with the Full-Scan graph showing when displayed peptide is deleted. - Fixed an unexpected error in the heatmap graph. - Fixed a problem introduced in 21.1 where transition list columns were not identified as numeric if the values were in quotes. (impacting LipidCreator) - Fixed Import Peptide Search FASTA page to hide panel for importing targets from a separate FASTA when not doing a DDA/DIA search. - Fixed a missing DLL issue with Percolator in MS Amanda DDA search. - Fixed storing calculated CE and DP values in .sky files with large target lists for Panorama. We think these improvements make Skyline 21.1 even better and hope you will update to this latest version soon. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan P.S. - Remember to register for the [Skyline User Group Meeting](https://skyline.ms/2021-ugm.url)

Skyline 21.1 Released

Thu May 27 12:00:33 PDT 2021

Dear Skyline Users, The Skyline Team is excited to give you Skyline 21.1, the product of another 7 months of effort in response to your feedback and use of Skyline. Over the past 7 months, you have started 11,000 instances (on average) of Skyline or Skyline-daily each week, and downloaded the software 1400 times per month. There have been 1000 posts to the support board. You showed your enthusiasm for Skyline Online twice, and the May Institute at NEU where some of you got a sneak peak at this release using Skyline-daily. Improvements in Skyline 21.1 include: - **New!** [DIA-Umpire](https://diaumpire.nesvilab.org/) integration with library-free DIA data processing. (thanks to the Nesvizhskii lab) - [[tutorial](https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/DIA-Umpire-TTOF-20_2_1.pdf)] - **New!** [Skyline Batch](https://skyline.ms/batch.url) for large-scale batch processing of data analysis with Skyline [[documentation](https://skyline.ms/batch-docs.url)] - **New!** [Class Discovery](https://skyline.ms/_webdav/home/software/Skyline/events/2017%20UW%20Course/participants/%40files/Day_3_am_10_30_Vitek_Statistical_Design.pdf#page=5) tools (hierarchical clustering and PCA plot) - [[documentation](https://skyline.ms/tip-clustering.url)] - Extended crosslinked peptide target support to allow any number of peptides and any number of links, especially important to monitoring disulfide bonds on antibody drug conjugates. - New UI for direct pasting or File > Import > Tranition List, allowing users to assign meaning to columns. - Improved Import > Transition List or Assay Library format detection to do a better job of detecting the list and decimal separators regardless of system number format settings. - Detection plot improvements. - New spectrum annotation button on the Full-Scan graph to allow full peptide fragment annotation on extraction spectra. - Added update progress display to RT > Regression and Scheduling plots. - Added calculated concentration y-axis on the peak area graph, found under right-click > Normalize To. - Added iRT support for command-line import peptide search. - Added View > Targets menu item to clarify how to get Targets back after closing, especially for small molecules. - Improved File > Share to avoid saving on unmodified documents and save directly to the .sky.zip file to avoid overwriting the file on disk for modified documents. - Enabled the --ui argument for SkylineCmd.exe to show the UI and allow changes that get stored in its user settings file. - Adding small molecules from View > Spectral Libraries where the library contains molecule list information will preserve the molecule list name. - Added optional display of ion mobility information in chromatogram graphs. - File > Export > Spectral Libraries now preserves protein and molecule list name information in the resulting .blib file. - Extended spectral library support: - Support for the latest DIA-NN speclib format. - Support for reading MSP-formatted spectral libraries as exported by Thermo's mzVault Viewer. - Support library building with .mzid.gz files and use it for MS Amanda DDA search in Skyline. - Support library building for invK0 attribute in pepXML written by PEAKS export. - Improved error message when a supported spectral library type (.msp, .sptxt, .hlf) is added as the file to use in building a library. - Added support for "RTINSECONDS" retention time encoding in an MSP spectral library file comment. - Improved error handling when trying to read a damaged BiblioSpec file. - Improved memory consumption during full-scan data import. - Added "Simple Ratios" checkbox to Peptide/Molecule Settings > Quantification settings. - Added new report fields: - Added TransitionResult.CycleTimeAcrossPeak report field. - Added Protein.ProteinSequenceCoverage report field with the percent of protein sequence amino acids contained in any of the peptides. - Added "Library Ion Mobility" report fields. - Added "TransitionResultIsQuantitative" and "TransitionResultIsMs1" report fields for MSstats. - Updated instrument vendor integration: - Updated Agilent method export format. - Updated the SCIEX WIFF2 DLLs. - Updated Waters MassLynx DLLs to 4.8 which returns profile IMS data with flanking zero points. - Ion mobility improvements found testing Thermo FAIMS support: - Negative CoV values now allowed. - On export of transition lists, CoV value now pulled from ion mobility library as needed. - Ion mobility libraries now support molecules described only as name+mass (was assuming a chemical formula would be available) - Viewing raw scan data now shows the scan's ion mobility value when available. - Populating an ion mobility library via "Use Results" works properly when two molecules shared the same name but different details - Other ion mobility UI fixes: - Fixed "Transition Settings > Ion Mobility > Use Spectral Library Ion Mobilities" checkbox to avoid state where it would not uncheck. - Full Scan graph now redraws on data reimport when showing ion mobility filter information, to ensure correct position of the purple IM filter band. - Fixed an issue with the Full-Scan view showing only one chromatogram type (MS1 or MS/MS) when both are available. - Fixed Edit Annotation form to display an error for a value list with not values specified. - Fixed opening or creating an ion mobility library file before the "Name" field is completed, an error pops up. - Fixed Import Peptide Search for PRM requiring MS1 filtering settings. - Fixed problem in number of methods created when exporting an isolation list or method for Thermo Fusion machines. - Fixed "Ratio to Heavy" to show up even if Heavy is not an internal standard type. - Fixed support for non-Unimod mods and terminal mods in DDA search with MS Amanda. - Fixed DDA search with MSAmanda to ignore FileNotFound/DirectoryNotFound when deleting temp files. - Fixed import peak boundaries into multi-sample wiff files. - Fixed pepXML spectral library building to accept search results from "peaks_db" as well as "peaksdb". - Fixed DDA search with MS Amanda fragment tolerance always using precursor tolerance units. - Fixed NullReferenceException pushing "Add" button from Result File Rules Edit List form. - Fixed issue with Refine >Associate Proteins with a nameless FASTA sequence. - Fixed unexpected error typing ')' into the empty element at the bottom of the Targets view. - Fixed MSFragger spectral library builder to prefer spectra from _uncalibrated.mgf to avoid de-charged fragment ion peaks. - Improved error message loading .skyd file when it is found to be corrupted. - Improved audit log hash calculation to avoid the possibility of duplication. - Fixed bugs with Turkish language settings mostly related to case insesitive pattern matching. - Fixed library build treating Mascot fixed terminal mods as not overridden by variable terminal mods. - Fixed an unexpected error when importing results with an ion mobility library when a precursor ion appears more than once in a document. - Fixed Waters "Unknown Generic Error" due to calling GetDriftTime() on functions existing in Waters .RAW but not listed in _extern.inf. - Fixed precursor ion spectrum support for WIFF files (use element instead of ). - Fixed unexpected error when user specifies a DDA search in the import wizard but then uses the "Back" button to start over. - Improved error handling when importing small molecule transition lists with inconsistent molecule descriptions. - Fixed unexpected error exporting method for Bruker timsTOF. - Fixed bug where Protein Abundance was always #N/A if normalization method is Ratio to Heavy. - Fixed a bug in the small molecule UI where inappropriate text was having "Peptide" replaced with "Molecule". - Fixed issues in handling loss-only modifications like water and ammonia: - Highlighting in the Targets view for loss-only modifications. - Not possible to specify loss-only modifications with Edit > Modify Peptide. - Importing Assay Libraries with loss-only modifications on peptides requiring explicit modifcations caused an error. - Fixed to force choosing a filename with the same extension when a library file is missing. - Fixed perf and error problems with "Remove Peak" on the Document Grid. - Fixed irtdb docxml bug. - Fixed DIA isolation scheme in Import Peptide Search to use the one currently set. - Fixed Import Peptide Search case with no results files used to create a template document for Skyline Batch. - Fixed to include PeptideSettings - Filter tab settings in Library Explorer - Add All button. - Fixed NullReferenceException displaying tooltip on Fold Change Volcano plot if document has small molecules. - Fixed library build from MaxQuant search results not applying terminal label-type mods. - Fixed custom formats on columns in the Document Grid would be forgotten as soon as the data was refreshed. - Fixed Mascot variable mod override logic in library build. - Fixed TIC Normalization on the Peak Area Replicate Comparison graph. - Fixed message for opening .sky file inside a ZIP file to work when the file is in a subdirectory. - Fixed bug preventing DDA search with multiple files of the same name. - Fixed "An item with the same key has already been added" exception changing Transition Settings in a document that has a molecule with multiple precursors that are the same as each other. - Fixed problem where DDA search incorrectly adds isotope modifications to the document as structural modifications. - Fixed problem where rdotp would not appear in the Targets tree if any of the heavy transitions had zero area. - Fixed problem where "Accuracy" is miscalculated if the Sample Dilution Factor is not 1. - Fixed unexpected error if using "Modify" menu item on a molecule and changing its chemical formula to result in some precursor transitions no longer existing in the mass distribution. - Fixed problem where non-quantitative transitions would not show up in Peak Area - Replicates view. - Fixed highlighting in red "Include all matching scans" if the Acquisition Method is "Targeted" when that is the right option. - Improved agreement between command-line error logging and non-zero exit codes. - Users running Chinese and Japanese language Skyline command-line should update SkylineRunner.exe - Fixed Tools > Options - Miscellaneous - Clear All Saved Settings for teaching and testing. - Fixed a Minimize Results error if it was opened while the document was still loading. - Fixed a sizing layout issue in the FASTA page of the File > Import > Peptide Search wizard. - Fixed unexpected errors in the RT scheduling graph. - Fixed Library Match title to contain library name again - broken when Prosit was added. - Fixed --report-invariant command-line argument to always use a comma field separator. - Fixed Import Peptide Search to add RT predictor in if adding existing library with iRT values. - Fixed Import Peptide Search to always show Match Modifications page. - Fixed notification of iRT calculator modification when using BLIB file. This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page: https://skyline.ms/skyline64.url And install this latest release. It should be worth the effort. (Please note: We are discontinuing 32-bit Skyline. This upgrade requires a 64-bit computer.) Thanks for your continued use, feedback, and support of the Skyline Project. Brendan MacLean Skyline Principal Developer

NEW! Skyline Batch 20.2

Wed Feb 03 17:50:19 PST 2021

Dear Skyline Users, We have released Skyline Batch 20.2.0.398 (thanks to our intern Ali Marsh), an entirely new user interface for running the batch processing Skyline workflow highlighted in multiple webinars and courses. An installation link and full documentation with tutorial examples adapted to Webinars 14 and 15 can be found on the following web page: https://skyline.ms/batch.url With this release, you no longer need to run .bat files in a Windows Command Prompt window to take full advantage of the power of the Skyline command-line interface for importing data files, exporting reports, and you can also run R scripts on those exported reports. This release works with Skyline 20.2 and Skyline-daily 20.2.1 releases. Give it a try and give us feedback. We hope you will enjoy the power of this new tool. Brendan MacLean Skyline Principal Developer

PATCHED: Skyline 20.2 (342 - 5be799340)

Tue Dec 08 12:08:19 PST 2020

Dear Skyline Users, Please upgrade! I have just released a patch to Skyline 20.2 with the following improvements over the initial release: - Finalized Chinese and Japanese translation text - Fixed canceling the ion mobility library editor form when there are errors - Fixed some issues with background loading of ion mobility libraries (.imsdb files) - Fixed NullReferenceException pushing "Add" button from Result File Rules Edit List form - Fixed DDA search fragment tolerance always using precursor tolerance units to allow searching hybrid data - Fixed an unexpected error in adduct parsing We think these improvements make Skyline 20.2 the best version of Skyline ever released, and we hope you will upgrade soon. Right now 95% of Skyline use is on 20.2, 20.1, or Skyline-daily. Though 18% is still from 20.1. So, UPGRADE!! Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy and thanks for staying current. --Brendan

Skyline 32-bit End of Line

Wed Oct 21 15:39:38 PDT 2020

Dear Skyline Users, Early releases of Skyline were 32-bit only, but now 32-bit releases of Skyline account for around 1% of startups. We would like to make Skyline 20.2 the last version of Skyline with a 32-bit installer. If you are using the 32-bit version of Skyline and feel this would be problematic for you, please email us and explain so that we can be sure to consider the position you are in. Or maybe use this to motivate your employer to upgrade your computer to allow you to stay current with 64-bit Skyline in the future. Otherwise, you should expect 32-bit releases of Skyline-daily to end during this next development cycle and Skyline 20.2 to be the last official release with a 32-bit installer. We will release all patches to Skyline 20.2 with 32-bit installers as usual. Thanks for using Skyline and all of the amazing feedback you have provided us over the past 11 years. --Brendan

Skyline 20.2 Released

Tue Oct 13 08:21:41 PDT 2020

Dear Skyline Users,

The Skyline Team is excited to give you Skyline 20.2, the product of another 8 months of effort in response to your feedback and use of Skyline.

Improvements since Skyline 20.1 include:

Integrated DDA Search (with MS Amanda) in Import Peptide Search wizard with tutorial
Support for crosslinked peptides (chemical crosslinking and disulfide bonds)
- Single-line modified peptide sequence format support for crosslinked peptide targets (supported in Edit > Insert > Peptides)
  - PEPTIDEA-PEPTIDEB-[+mass@a,b]
  - e.g. PETKPESER-EKVLTSSAR-[+138.06808@4,2]
- Support for loop-links, e.g. AKIQDKEGIPPDQQR-[+138.06808@2-6]
- Spectral library building support for Proxl XML (http://proxl-ms.org/) of crosslink peptide seaches
Result File Rules - automated annotation population from result file properties including File Name and File Path
View > Detection > Replicate Comparison and Histogram plots for applied mProphet models
Qualitative ion ratio support
iRT improvements
- "Automatic" option for iRT standard during library building
- Non-linear iRT - adding Lowess and Logarithmic regressions
- Improved iRT handling - especially with CiRT - for File > Import > Assay Library
- Edit iRT Calculator improvements:
  - Add new IrtStandard using the current calculator's standard peptides
  - Store best transitions and relative ion abundance with calculator
Made Explicit Retention Time Window limit the range in which peaks are considered.
Support Thermo SureQuant using Transition Settings > Instrument > Triggered acquisition checkbox
File > Export > Method support for Bruker timsTOF prm-PASEF methods
IMS filtering settings moved to Transition Settings - Ion Mobility.
Added "Protein Results" -> "Protein Abundance" column to reports to expose the protein value used by the Group Comparison framework.
A new Refine > Advanced - Group Comparison tab making it easy to perform the group comparison refinement demonstrated in Webinar 8 (through Refine > Accept Peptides and a bunch of copy-paste operations)
Remove based on CV cutoff removes empty peptides
Refinement based on CV and GC can still remove proteins based on remaining peptide count
Added Prosit support for Propionamide (C)
Added a "Product Neutral Loss" column to small molecule transition list reader, which makes it convenient to describe fragments in terms of a chemical formula to be subtracted from the precursor's chemical formula.
Reduced the number of columns shown by default in the small molecule Insert Transition List grid
Import Peptide Search Wizard added from and to transition filters and min and max instrument m/z values
Spectral library building for the DiaNN specLib format.
Added support for Golm Metabolome Database GCMS spectral library in .MSP format available at http://gmd.mpimp-golm.mpg.de/
Support even more MSP spectral library format variants for small molecules
Support for specifying the analyte concentrations for each target by replicate in calibration curves with PeptideResult.ExplicitAnalyteConcentration
Added apply peak to group
Added list editing buttons to the Document Settings - Reports tab
Restored the ability to specify Explicit Collision Energy at the precursor level.
Decoys checked against targets and warning presented with ability to regenerate if they don't match closely enough.
Added View > Chromatograms > Close All and keyboard short cuts for Close (Ctrl-F4) and Close All (Ctrl-Shift-F4)
Removed limit on number of peptides and transitions during File > Import > FASTA - counting on the user to cancel the operation when it is doing more than expected.
Improved support for MS1-only TIC and BPC
New resizing progress form to show all status text
New report values in PrecursorResultsSummary for Detection Q Value (min, max, median)
Refresh of all links and images for tutorials in the Start Page - Tutorials form
Some performance improvements for very large DIA documents.
Command-line not import a raw file from the same path unless a replicate name is specified with --import-replicate-name
Command-line support for --decoys-discard
Command-line support for --refine-cv-remove-above-cutoff with decimal percent if value <1
Improved handling of invalid entries in spectral libraries - warn and filter instead of failing to load
Many smaller bug fixes such as:
- Fixed failure to annotate fragment ions in heavy labeled Prosit predicted spectra.
- Fixed failure to match m/z values between heavy labeled library spectra and Prosit mirror plot spectra.
- Fixed handling of small molecule .MSP library files without Precursor_type values.
- Fixed reading LipidBlast .MSP files from MoNA
- Fixed support for MaxQuant's NotNTerm and NotCTerm fixed mods
- Fixed bug where MaxQuant spectral library build failing to parse file if it is missing both optional columns "Labeling State" and "Evidence ID".
- Fixed library build mzML -> MSFragger -> PeptideProphet pipeline (broken by previous fix to TIMS/MGF -> MSFragger -> PeptideProphet; now both pipelines work)
- Fixed library build file extension detection to be case insensitive.
- Fixed library build for tilde quotes ("File:~SomeRunName~") in Mascot DAT parser.
- Fixed library build for ProxlXml parser to not require linker_mass for unlinked peptides.
- Fixed a problem reading Agilent GCMS SIM SIC chromatograms
- Increase the threshold scan range at which we consider an MS1 scan to be a "SIM Scan" from 200 to 500
- Fixed SkylineCmd.exe error reporting when Skyline[-daily].exe are missing and ability to run from downloaded ZIP file without needing to unblock more than SkylineCmd.exe itself.
- Fixed possible deadlock using SkylineCmd/Runner to import data
- Fixed calculation of TIC when not MS1-only TIC is available - temporarily reverting to old slower Skyline code to calculate through spectrum summing - faster fix coming
- Fixed export of negative CoV values for FAIMS methods
- Fixed IMS display and units in reports to be consistent across PrecursorResults and Chromatogram values
- Fixed a null reference when dealing with libraries that have inconsistent ion mobility coverage
- Fixed errors requiring a restart switching iRT standards in the Edit iRT Calculator form
- Fixed preserving the original standards in an iRT library when standards are changed with the dropdown list
- Fixed warning about overwriting changes in an iRT library when none have been made
- Fixed exception using triggered acquisition if some precursors are missing chromatograms.
- Fixed unhandled error when importing peak boundaries for document with no result files
- Fixed issues handling SCIEX Midas data
- Fixed mProphet model training display to avoid empty space on the left and compressed histograms on the right.
- Fixed "Bandwidth too small" exception doing a Loess regression if there are not enough peptides in the document.
- Fixed LOQ determination so that it starts looking from the highest concentration point stops looking once it finds a level that fails the criteria.
- Fixed Shimadzu method numbering
- Fixed Ctrl-A to work as select all in the Document Grid even when it is docked.
- Fixed loading Shimadzu SRM files with just 1 chromatogram.
- Fixed exception bringing up RT Linear Regression window if there are crosslinked peptides in the document.
- Implemented a workaround for 32 transition limit on Waters method functions.
- Fixed handling a couple of novel adduct descriptions seen in the wild, e.g. "(M+H)+" and "(M+H)+[-H2O]", which would normally be written as "[M+H]+" and "[M-H2O+H]+" respectively.
- Fixed NullReferenceException trying to use Triggered Acquisition in small molecule document.
- Fixed retention time alignment makes mouse act out of phase on aligned replicate chromatogram graphs.
- Fixed File > Import Assay Library recognizing sequences surrounded by underscores and preceding N-terminal modifications produced by Spectronaut.
- Fixed pepXML reader looking for pepXML elements inside <analysis_summary>.
- Upgraded MethodCreator.dll for Agilent method export.
- Fixed Panorama server checking for in-house Panorama servers.
- Fixed tooltips on Molecule Settings form for small molecules.
- Fixed blank IMS spectrum Full-Scan plot when shown in 2D with filtering on.

This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your continued use, feedback, and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer

PATCHED: Skyline 20.1 (155 - a0e7323e3)

Wed Jun 03 14:04:22 PDT 2020

Dear Skyline Users, We hope you are enjoying ASMS and thanks again for making the user group meeting this year such a special one. I have just released the second patch to Skyline 20.1 with the following improvements over the initial release: - Fixes to Prosit integration handling of heavy labeled peptides - Fixed failure to annotate fragment ions in heavy labeled Prosit predicted spectra - Fixed failure to match m/z values between heavy labeled library spectra and Prosit mirror plot spectra - Fixed BiblioSpec's mzML -> MSFragger -> PeptideProphet pipeline (broken by previous fix to timsTOF/MGF -> MSFragger -> PeptideProphet) - Fixed error handling for SkylineCmd.exe, especially when installed from a network downloaded ZIP file - Fixed formatting of calculated concentration of CalibrationForm so that it displays the units and four decimal places. - Fixed wrong version of Agilent MethodCreator.dll for SRM method export. - Fixed validation errors in Edit Irt Calculator form when switching standards using the dropdown list. - Updated tutorial images and links in the Start form. We expect this to be the last patch to Skyline 20.1, which we really think was a major release for us and worth the upgrade, if you are still using an earlier release. As explained at the Skyline User Group Meeting last week, we are making an effort to update all of our tutorials to this release. UPGRADE!! Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

PATCHED: Skyline 20.1 (76 - 0d62152d0)

Mon Mar 16 19:09:58 PDT 2020

Dear Skyline Users, I have just released a patch to Skyline 20.1 with the following improvements over the initial release: - Finalized Chinese and Japanese translation text - Fixed preserving manually set peak boundaries after reimport - Fixed Library Match view visibility to require a library or Prosit enabled - Fixed undo and audit logging of right-click > Quantitative property setting - Fixed command-line import deadlocking race condition - Fixed modification redefinition error in Import Peptide Search - Fixed major performance issue with lockmass correction in Waters data imports - Fixed command-line logic for when files get ignored during import if they have already been imported - Fixed Bruker data import failure issues - Fixed issue where Transition Settings changes could be overwritten during Import Peptide Search - Fixed audit logging of changes to DIA isolation schemes - Fixed a null reference when dealing with libraries that have inconsistent ion mobility coverage - Fixed exception in the iRT calibration form - Fixed exception doing "close all chromatograms" - Fixed Import Peptide Search to turn off MS1 filtering if no precursor ions - Fixed command-line run length to decimal value instead of an integer We think these improvements make Skyline 20.1 even better and hope you will update to this latest version soon. Skyline should ask you to update the next time you restart or use Help > Check for Updates. Enjoy. --Brendan

Skyline 20.1 Re-Released

Thu Jan 30 20:45:19 PST 2020

Dear Skyline Users, In order to fix an issue with the Prosit Server address released in Skyline 20.1.0.28, I have just released Skyline 20.1.0.31 along with a fix to the Help > About image (which was left as Skyline-daily), the year which was left 2019, and a requested fix to make --exp-run-length a decimal value instead of an integer. All minor changes. If you have already upgraded, then this should be a minor automatic upgrade the next time you restart or use Help > Check for Upgrades. Otherwise, you shouldn't even notice this and you will still want to manually upgrade from 19.1 or 4.2. Thanks for reporting the issues, and thanks to those of you who have already upgraded. --Brendan

Skyline 20.1 Released

Tue Jan 28 19:32:56 PST 2020

Dear Skyline Users,

The Skyline Team is excited to give you Skyline 20.1, the product of another 6.5 months of effort in response to your feedback and use of Skyline.

Improvements since Skyline 19.1 include:

Prosit spectrum and iRT prediction support directly integrated into the UI
- Building libraries for targeted peptides in a document through Peptide Settings - Library - Build button.
- Prosit spectrum prediction viewing in the Spectrum Match plot with new right-click menus, including mirror plotting
- Settings in Tools > Options > Prosit
Support for spectral library building from MS Fragger pepXML search results
Support for diaPASEF!
- We have run this with 2 separate 3-organism datasets through the LFQBench statistical assessment and that works.
Improved ddaPASEF and initial prmPASEF support.
Performance gains in importing Agilent and Waters IMS data as much as 2x or more.
Parallel file import with proteomewide DIA in the UI or by default on the command-line has performance similar to what was previously only available from the command-line using --import-process-count. Choose "Many" on your next import or just ignore threading the next time you import from the command-line.
Optimized spectrum memory handling for instrument vendors with .NET data reader libraries, benefitting Agilent, SCIEX, and Thermo
A new "Consistency" tab in the Refine > Advanced form, supporting CV and q value cut-offs
New checkbox for Refine > Advanced - Results tab Max precursor peak only
Support for Multiple Attribute Model (MAM) grouping with Peptide.AttributeGroupID and PeptideResults.AttrributeAreaProportion
Added File.SampleID and .SerialNumber (of the instrument) as fields in Document Grid custom reports
Transitions Settings - Full-Scan - MS/MS filtering has been extended to apply to all non-MS1 spectra (e.g. MS3) as long as the MS1-level precursor matches the target precursor m/z The redundant library filtering phase of spectral library building is around 20x
Improved iRT calibration UI making it easy to create new sets of standards based on existing sets that can be used in spectral library building and the Import Peptide Search wizard
More iRT improvements including more intelligent use of 80+ CiRT peptides when CiRT is chosen during library building
New right-click > Quantitative menu item for changing the Quantitative property on transitions in the Targets view TIC and BPC now come from raw data files and do not need to be extracted from MS1 spectra which has performance benefits for MS1 filtering
New global "QC" transitions have been added such as the pressure trace
Calibration curve fixes to make ImCal (Isotopolog Calibration Curves) work
New "Calculated" annotations have been added which support storing Skyline calculated values in annotations for future use with AutoQC
Optional display of spectral library spectrum scores in Spectrum Match, View > Spectral Libraries and in Document Grid
Added Spectral library building support from "Assay Library" TSV
New View > User Interface menu item in case the user misses the toolbar button
New View > Peptides submenu to display modifications in the Targets view text for cases like glycan mods on biologics
Support for charged losses on peptide modifications like for glycan mods to monitor precursor - lost, minus charge
New option to order by m/z in exported methods/lists for optimized quadrupole switching Restore the ability to insert a transition list of either type when not in mixed UI mode
Support KEGG IDs as molecular identifiers in small molecule targets.
Improved support for D used in chemical formulae in place of the Skyline default H'
Added support for Thermo Exploris and Eclipse instruments
Support for opening .skyp files downloaded directly from Panorama
New command-line arguments:
- --version - prints the Skyline[-daily] version information to the console
- --save-settings - saves and settings changes made during the session (e.g. opening a document may add elements to lists)
- --tran-predict-ce="<name>" - change the Transition Settings - Prediction - Collision energy setting
- --tran-predict-dp="<name>" - change the Transition Settings - Prediction - Declusering potential setting
- --tran-predict-cov="<name>" - change the Transition Settings - Prediction - Compensation voltage setting
- --tran-predict-opt="<name>" - change the Transition Settings - Prediction - Optimization library setting
- --import-filename-pattern - selects imported files from directory by a pattern
- --import-samplename-pattern - selects imported samples from a multi-file WIFF by a pattern
- --ims-library-res command-line argument for adjusting the library IMS extraction resolving power for testing varying settings on 3-organism mixes
- --share-zip - fixed from being broken in 19.1
- --exp-order-by-mz - orders transitions in exported methods/lists by m/z for optimized quadrupole switching
Strong versioning in Skyline-daily.exe and SkylineCmd.exe
- When you hover the mouse over these EXE files in Windows File Explorer the version number is reported in a tip (no longer just 1.0.0.0)
- The command-line --version argument now always reports a full version, even for a "developer build" including the Git hash for the source control revision on GitHub, and now the version of ProteoWizard, ensuring the pwiz_data_cli.dll can be loaded.
- The Skyline Help > About form now also includes this full version with Git hash
Many smaller bug fixes such as:
- Spectral libraries from MaxQuant results using spectra from raw data now uses the right spectra
- Fixed BiblioSpec parser for MaxQuant 1.6.7 mod format
- Fixed for issue with iProphet and 2H element for MaxQuant
- Made charge state suffix parsing more flexible to handle the following cases:
  - A series of + or - symbols however long (used to stop at ++++ for positive and -- for negative)
  - Use CultureInfo.TextInfo.ListSeparator (semi-colon in Europe) "; +5" instead of CultureInfo.NumberFormat.NumberGroupSeparator (period, space or apostrophe in Europe) ". +5", " +5", or "' +5"
  - Allow invariant form always ", +5" even when current culture indicates "; +5"
  - Allow the absence of the space in charge states with numbers, i.e. ",+5" or ";+5"
- Fixed right-click > Order By > Annotation in replicate summary plots
- Fixed error "Spectrum must have a source file" when doing Import Assay Library tutorial
- Fixed problem where "batch_name" was not getting written out for replicates.
- Fixed problem where changing the uniqueness constraint in the Peptide Settings dialog does not result in a new Undo record being created.
- Fixed error when doing "Export Annotations" if StandardType has been specified for peptides.
- Fixed error when List has "value list" column type.
- Exclude peptides from .elib files that do not appear in the "PeptideQuants" table.
- Fixed missing peak logic when importing with EncyclopeDIA or OpenSWATH results
- Added support for reading the expect score from Comet pepXML and for using ms2 files for finding spectra of pepXML files.
- Fixed Tools > Tool Store error message when skyline.ms server is down for maintenance.
- Fixed controls hidden on Import > Peptide Search form when initiated from the Start page.
- Fixed problem where Skyline was not acknowledging the isolation windows on MSX scans.
- Fixed calculation of LOD. It was incorrectly using only using the multiple of the SD of the blank values. It was forgetting to add the mean of the observed values as well.
- Fixed Precursor Concentration getting blanked out whenever the Peptide Settings changed.
- Fixed to support a change to the Uniprot interface for querying protein details.
- Fixed exception when doing "Pick Children" on a small molecule that has two identical precursors.
- Fixed "Refine > Advanced" max peptide peak rank when there are peptides that only have internal standard precursors and increase maximum peptide peak rank from 10 to 20.
- Fixed exception that can happen if deselect EmptyNode at bottom of Targets tree while Peak Area Replicate Comparison is shown.
- Fixed CCS calculation for Bruker data to use 2*N instead of just N.
- Fixes to improve support for a 1.3 GB Assay Library including a fix to an OutOfMemoryException
- Fixed progress display of upload to Panorama
- Fixed Area CV calculation for heavy labeled ratio normalization.
- Fixed modified peptide sequence text exported from Skyline in .blib spectral libraries to match library builds
- Fixed unexpected error using Refine > Advanced in small molecule documents with results
- Fixed renaming a molecule causes miscalculating mass of transition with heavy label adduct
- Fixed File > Export > Spectral Library losing information from small molecule documents
- Fixed case sensitivity in library file name extensions

This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your continued use, feedback, and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer

Skyline 19.1 Released

Sun Jul 14 23:34:23 PDT 2019

Dear Skyline Users,

I have just released Skyline 19.1, the product of another 8 months of effort by the Skyline team in response to your feedback and use of Skyline. This is the 19th official release and the first of 2019. So, for this 10th anniversary realese, we are changing to a year-based version number like many other mature products.

Improvements since Skyline 4.2 include:

New! Small molecule and proteomics UI modes [introduction]
- And a form that asks for your preferred mode once
iRT and Optimization library support for small molecules
New! Lists - define lists of values in multiple columns and associate them with elements in your documents through annotations.
- See Document Settings – Lists
Batch calibration
Import > Peptide Search with an existing library (including EncyclopeDIA .elib files)
A new MS/MS filtering Acquisition method named "DDA" which sets all fragment ions to non-quantitative and does not truncate MS1 chromatograms the way "Targeted" (or PRM) does.
Edit > Refine became a top-level Refine menu between Edit and View and got reorganized for ease-of-use.
The Document Grid "Views" menu has been changed to "Reports" to better align with File > Export > Report and Document Settings - Reports
Added Actions menu to the Document Grid to enable bulk peak removal based on filtering
New command-line help for SkylineRunner/SkylineCmd available with --help argument and Help > Documentation > Command Line in Skyline
Command-line support for Refine > Advanced options
Command-line support for setting precursor charge states, fragment charge states and fragment types
Moved some explicit parameter values like CE from precursor to transition level
Audit log improvements to support working with Panorama and tampering detection
Building a library from MaxQuant msms.txt now attempts to find the original spectrum source files and use the spectra in them to avoid using charge state deconvoluted spectra, but allows the user to override this default if the spectrum source files cannot be found
A new <Edit current...> choice in the dropdown lists in Edit > Modify Peptide to make updating specified modification definitions easier
Improved handling of common background proteome building problem where user tries to open or create the FASTA file causing it to be overwritten by an empty PROTDB file
Changed File > Share default to "Complete" instead of "Minimal"
Add "PeptideResult.ModifiedAreaProportion" which is the normalized area of the PeptideResult, divided by the sum of the other NormalizedAreas for all of the other PeptideResults in the same replicate and protein that have the same unmodified sequenceAdded new Transition.LossFormulas field
Allow grouping by built-in properties such as "concentration" in addition to annotations in peak area graph
Many smaller bug fixes such as:
- Fixed to support C-terminal modifications in MaxQuant msms.txt
- Fixed library building for PeptideShaker results
- Fixed to add the .wiff2 extension to File > Import > Results form
- Fixed to support File > Export > Method for Thermo Altis
- Fixed to allow package installation for R external tools (like MSstats) in China
- Fixed for calibration curve text exported to report CSV files on Chinese and Japanese systems
- Fixed library building from paths with extended characters
- Fixed for spectral library building of Peaks mzIdentML/MGF export
- Fixed library building support for ProXL cross-linked peptides with PTMs
- Added support for radioactive 14C labeling as C"
- Added support for deuterium as D and H' and tritium as T and H"
- All elements in the periodic table now allowed in chemical formulae
- Fixed for q value cut-off advanced option in group comparison definition form
- Fixed to apply chromatogram transformation to non-quantitative chromatograms to match quantitative chromatograms
- Fixed for invalid precursor transitions after changing Full-Scan settings
- Performance improvement for importing large small molecule transition lists
- Fixed to Support new variant of retention time specification in NIST .msp library format
- Fixed audit log saving to use write and rename to avoid log truncation
- Fixed audit log enabling to create undo records and be more persistent
- Fixed to handling of invalid adduct specification
- Fixed to small molecule persistence with multiple keys
- Fixed undo/redo of setting standard type
- Fixed problem where modifications with negative mass cannot be found in iRT database (reported by Anatoly, thanks to Nick)
- Updated UIMFLibrary DLLs to version 3.6.6
- Fixed library build support for reading MaxQuant fixed peptide-N/C-terminal modifications
- Fixed parsing of pS/pT/pY variant of phospho mods from MaxQuant
- Fixed issue parsing PLGS final_fragment.csv modifications with paren’s in the mod name
- Fixed problem with implicit modifications not being included in "Modified Sequence" column in Document Grid
- Fixed importing report layouts from a .skyr file
- Fixed reading Shimadzu QTOF files that also open with the QQQ reader DLL
- Change SCIEX centroiding to multiply Y (area) values by 100 to make the numbers more similar to profile extraction (requested by SCIEX)
- Fixed Area CV histograms to ignore precursors with no chromatograms rather than Calculating... forever
- Fixed to continue importing chromatograms when iRT regression fails as long as chromatogram extraction is not dependent on it

This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your continued use, feedback, and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer

PATCHED: Skyline 4.2 (19072)

Mon Apr 08 19:12:56 PDT 2019

Dear Skyline Users: I have just released a patch to Skyline 4.2 (version 4.2.0.19072) with the following changes: - The 32-bit installers have been fixed to again support File > Import > Results. - The library builder has been fixed to again support PeptideShaker search results. That's it. Thanks to the 85% of you already using 4.2 or Skyline-daily. For the remaining 15% now it is really time to **UPGRADE**. We are confident that 4.2 is better than its predecessors. If you are not using Skyline 4.2 yet, please follow the manual steps to UPGRADE now. If you are already using Skyline 4.2, Skyline should ask to upgrade the next time you restart or use Help > Check for Updates. If you are at all interested in the Skyline small molecule support, then you owe it to yourself to try Skyline-daily. It now has 3 UI modes: proteomics, small molecule and mixed (see attached). Try it and give us feedback on how you like working without all the protein and peptide references in the original Skyline proteomics-centric UI. Enjoy using Skyline in your research. --Brendan

RE-PATCHED: Skyline 4.2 (19009)

Wed Jan 09 17:39:39 PST 2019

Dear Skyline Users, I have just released an updated patch to Skyline 4.2 (version 4.2.0.19009) to fix an installation issue (impacting Windows 7 systems) with yesterday's patch release. If you upgraded to the last patch, Skyline should ask to upgrade the next time you restart or use Help > Check for Updates. Otherwise, all benefits and instructions from the last release continue to apply. Please upgrade! Thanks to the people using Windows 7 who reported it so quickly. --Brendan

PATCHED: Skyline 4.2 (19008)

Tue Jan 08 16:31:54 PST 2019

Dear Skyline Users: I have just released a patch to Skyline 4.2 (version 4.2.0.19008) with the following changes: - Final 4.2 software translations for Chinese and Japanese - Fixes for SCIEX WIFF2 support - Fixes to Shimadzu Q-TOF installation and seconds-to-minutes in retention times - Add Thermo Altis method export support - Fix for Waters UNIFI - Fix iRT regression failure warning behavior - Fix spectral library building for MaxQuant C-terminal mods - Fix spectral library building for MaxQuant missing mod from no user feedback to error - Fix image scaling from some toolbar buttons which was causing layout problems - Fix command-line WIFF import failure handling causing silent exit with AutoQC Loader - Fix RInstaller network connection detection for China If you are not using Skyline 4.2 yet, please follow the manual steps to UPGRADE now. If you are already using Skyline 4.2, Skyline should ask to upgrade the next time you restart or use Help > Check for Updates. Thanks for using Skyline and staying current. --Brendan

Skyline 4.2 Released

Thu Nov 01 20:43:06 PDT 2018

Dear Skyline Users,

I have just released Skyline 4.2, the product of another 9 months of effort by the Skyline team in response to your feedback and use of Skyline, and the 18th release in 10 years. The first was Skyline 0.1, made to our collaborators at Vanderbilt University who were funding the project as part of NCI-CPTAC.

Here are the improvements we hope you will enjoy using soon and into a productive 2019. We encourage you to join the 2,300 users signed up for Skyline-daily to get early access to the newest features as we add them. Their testing and use accounting for 20% of all start-ups helps us feel confident you will enjoy this upgrade, which includes the following improvements:

AUDIT LOGGING - yes, really [documentation]
New Figures of Merit section in Peptide Settings – Quantification tab
- New LOD and LOQ fields in reports
- New display in Calibration Curve plot
New calibration features
- Regression fit = Linear in Log Space
- Single-replicate calibration with isotope labeled standards for system suitability
- Added Sample Dilution Factor field to Replicates in Document Grid for dilution of a sample to bring it within the linear dynamic range
Support for importing OpenSWATH results through File > Import > Peptide Search - DIA wizard [details]
Support for using integration boundaries and peak scores from OpenSWATH and EncyclopeDIA
Drift time predictor training from Use Results fixed for small molecules
Instrument support improvements:
- Agilint - support for negative ion mode QqQ data
- Bruker - timsTOF support for PASEF, All Ions, and PRM
- SCIEX - support for new SCIEX WIFF2 file format & clearer method export, CE and DP settings
- Shimadzu - support for 9030 Q-TOF and 8045 QqQ
- Thermo - support for Thermo FAIMS, GC-MS, Tune v3+ compatibility, and faster raw file reader DLL
- Waters - advances in SONAR and CCS calibration and importing data from UNIFI server
Settings > Integrate All no longer affects Precursors.TotalArea nor other quantitative metrics. At last, it is just visual.
File > Import or Export > Annotations for importing or exporting annotations values directly from or to a CSV file
New command-line support
- --import-document = File > Import > Document
- --import-annotations = File > Import > Annotations
- --share-zip = File > Share
- --import-all-files = File > Import > Results of all files in the directory specified, but not subdirectories
- --import-all[-files] and --import-replicate-name together to import multiple files into a new replicate
- --reintegrate-exclude-feature = unchecking feature in mProphet model
New library build support
- Mascot error tolerant searches and PASEF searches
- MassIVE mzTab
- MetaMorpheus mzIdentML
- Crux Percolator pepXML
- PEAKS pepXML/mzXML export when scans are out of order
- Proteome Discoverer ExpectationValue support and pdResult files with multiple workflows
- MaxQuant deuterium labeling modifications and results lacking Labeling State column
Added new iRT standard mix RTBEADS
Added ability to separate CVs in Peak Areas > CV Histogram by precursor or fragment ions in mixed MS1 and MS/MS documents
Added Plot Type > Residuals to Retention Times > Alignment view
Faster volcano pot updates and format filtering peptides by protein attributes
Mouse centered zooming added to some graphs that did not yet have it
Edit > Delete of transitions removes matching transitions in matching reference precursors
Edit > Refine > Advanced new option to remove peptides without a matching spectrum
Added find support for report link columns with text display
Increased maximum fragment charge state to 20 for whole protein MS/MS
Increased custom molecule maximum mass from 100 KDa to 160 KDa
Added a new copy button in the lower-left corner of message boxes to make it clearer that form contents can be copied as text
Many smaller bug fixes [read more]

This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your continued use, feedback, and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer

PATCHED: Skyline 4.1 (18169)

Tue Jun 19 16:15:01 PDT 2018

Dear Skyline Users, I have just released what I really hope is the final patch to Skyline 4.1 (version 4.1.0.18169) with the following changes: - Reverted the product name from "Skyline-daily" back to just "Skyline" - Fixed a bug where libraries were disregarding modifications when returning retention times (reported by Matt, thanks to Nick) - Fixed matching spectra in SCIEX Midas data to precursors with modifications, especially heavy labeled (reported by Cathy, thanks to Nick) - Fixed Peptide Settings for Waters Sonar data (reported by Roy) Most of these got fixed a while ago but were lost when our project transitioned to a new source control system. If you are already using Skyline 4.1, Skyline should ask to upgrade the next time you restart or use Help > Check for Updates. Thanks for the quick issue reports. Sorry for the extra confusion around the last patch. --Brendan

PATCHED: Skyline 4.1 (18163)

Thu Jun 14 12:54:41 PDT 2018

Dear Skyline Users: I have just released what we expect to be the final patch to Skyline 4.1 (version 4.1.0.18163) with the following changes: - Final translations for Chinese and Japanese - Fix to a bug that caused miscalculation of m/z values for fragments with losses when Skyline needed to recalculate these (not the first time) If you are not using Skyline 4.1 yet, now is the time to UPGRADE. Already 90% of all Skyline instances started are 4.1 or Skyline-daily. If you are already using Skyline 4.1, Skyline should ask to upgrade the next time you restart or use Help > Check for Updates. Thanks for using Skyline. Great seeing so many of you at ASMS. --Brendan

Stuck on Skyline 3.7?

Mon May 14 21:33:01 PDT 2018

Dear Skyline Users, When we released Skyline 4.1, some users reported trouble opening small molecule documents created in version 3.7 or earlier. We have corrected all known small molecule backward compatibility issues in the current Skyline-daily release, but not all of those fixes are in the official Skyline 4.1 release. If you are a small molecule user still using version 3.7 due to problems you have experienced with 4.1, can you please contact me (bspratt@proteinms.net)? If we do not hear from anyone, we will assume everyone affected is now using Skyline-daily or has found another workaround (e.g. recreating documents in 4.1), and we will not bother to include the backward compatibility fixes in our next 4.1 patch release. Many thanks, Brian Pratt

PATCHED: Skyline 4.1 (11796)

Sun Feb 18 12:58:28 PST 2018

Dear Skyline Users, I have just released a patch to the Skyline 4.1 release to fix the following issues: - Fix upgrading 3.7 small molecule document with mixed polarities (thanks to Brian) - Fix upgrading 3.7 small molecule document to recognize user-provided formula like "C10H30Si5O5H-CH4" as equivalent to "C9H27O5Si5" (thanks to Brian) - Fix unexpected error handling heavy labeled small molecules (thanks to Brian) - Increase maximum custom molecule mass from 100 KDa to 160 KDa (requested by Lisa, thanks to Brian) - Fixed selection in area replicate comparison when grouping by annotation (reported by Shimin, thanks to Tobi) - Fix missing OK and Cancel buttons in Japanese version of Transition Settings (reported by Tokumaru, thanks to Brendan) - Fix issue matching newly built spectral library with 4-digit modification precision (thanks to Nick) - Fix yeast protein details lookup to use new Uniprot interface (thanks to Brian) - Fix unexpected error with more than 4 isotope label types (thanks to Nick) - Fix unexpected error for invalid prefix or suffix during import results (thanks to Kaipo) - Fix unexpected error in Peak Area CV toolbar (thanks to Tobi) - Fix unexpected error DDA retention time alignment (thanks to Nick) - Fix unexpected error "item with the same key already added" editing custom molecule (thanks to Nick) - Fix two modifications defined on the same amino acid can cause an error "The expression 'C''2H6N'' is not a valid chemical formula" (reported by Rich, thanks to Nick) - Fix handling when there are zero spectra in the spectral library to load and not cause an error (thanks to Nick) If you have already upgraded to 4.1, Skyline should ask to upgrade to the patch automatically the next time you restart or use Help > Check for Updates. Otherwise, now is a great time to upgrade to 4.1. Though it requires installing over your current Skyline, which you can do from the website installation page. --Brendan

Skyline 4.1 Released

Thu Jan 11 17:31:01 PST 2018

Dear Skyline Users,

I have just released Skyline 4.1, the product of another 7 months of dedicated effort by the Skyline team in response to your feedback and use of Skyline.

Here are the improvements we hope you will enjoy using through the first half of 2018, and we encourage you to join the 1,800 users signed up for Skyline-daily to get early access to the newest features as we add them. Their testing helps us feel confident you will enjoy this upgrade.

Improved small molecule support [detail slides]
- Support for NIST and self-built (from SSL format) small molecule spectral libraries with fragment annotation
- Neutral molecules with multiple precursor adducts
- Improved support for pasting small molecule transition lists with column headers
Bruker TIMS support that parallels IMS support for other vendors
A new Document Grid pivot editor and saved report layouts [detail slides]
Improved Import Peptide Search wizard for DIA with DDA for the mProphet workflow
File > Import > Assay Library makes importing Assay Library files easier than File > Import > Transition List
More performance improvements (memory use and speed) for large-scale DIA data processing
Interactive volcano plots for group comparisons with custom formatting [detail slides]
Interactive peak area CV histogram plots [detail slides]
High precision modification delta-mass support past a single decimal place
Points across the peak and manual integration adjustment visualizations in chromatogram plots [detail slide]
New line plot modes for summary (Replicate and Peptide Comparison) plots
Synchronized zooming available in summary (Replicate and Peptide Comparison) plots
New Import Results common prefix and suffix removal UI with real-time replicate name display
New delete button (red X) on the Document Grid
- allows deletion from the Targets View (proteins, peptides, precursors and transitions)
- filter and delete.
Possible to rename replicates from Document Grid (including copy-paste) with "Replicate Name" field
New "Exclude From Calibration" column on PeptideResult
New Quantitative column on Transitions [detail slides]
New non-blocking background population of Document Grid with full support for chromatogram values (times, intensities, mass errors) in Live Reports, both interpolated and raw values
New Edit > Integration menu with shortcuts for Remove Peak and Apply Peak to All
Display an informative warning when iRT calibration fails during import
Improvements for library building from peptide search formats which do not support probability cutoffs to make sure they get ordered correctly
Many other fixes...

This release may require a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your continued use, feedback and support of the Skyline Project.

Brendan MacLean
Skyline Principal Developer

PATCHED: Skyline 3.7 (11371)

Sun Sep 10 14:07:57 PDT 2017

Dear Skyline Users, Already, over 85% of Skyline use is either Skyline 3.7 or Skyline-daily. If you aren't using either yet, now is the time to see what you have been missing. (install directly from http://skyline.ms/skyline64.url) I have just released Skyline 3.7.0.11371, a patch to the original Skyline 3.7 release with several important bug fixes and finalized Chinese and Japanese translations. Fixes include: - Fix problem with chromatograms with more than 65535 points (thanks to Nick) - Fix some issues with Thermo MSF files (thanks to Kaipo) - Fix error message text when newer document format is not supported (thanks to Nick) - Fix regression in chromatogram matching introduced in 3.7 - Fix chromatogram library support for libraries created with 3.7 (thanks to Nick) - Fix unexpected error re-importing results with altered drift time filter (thanks to Brian) If you are already using version 3.7, Skyline should ask to update the next time you restart or use Help > Check for Updates. Thanks for using Skyline and especially thanks to all of you who have reported issues or posted exceptions when you got an unexpected exception message. --Brendan

Skyline 3.7 Released

Mon Jun 12 22:27:07 PDT 2017

Dear Skyline Users,

I have just released Skyline 3.7, the product of another 7 months of dedicated effort by the Skyline team in response to your feedback and use of Skyline.

Thanks for a great ASMS and all the inspiring new uses to which you are putting our software. We came home excited and inspired for the next product cycle, with plenty to do.

For now, though, here are the improvements we hope you will enjoy using through the second half of 2017, and we encourage you to join the 1,500 users signed up for Skyline-daily to get early access to the newest features as we add them.

Extensive performance improvements in speed and memory use for proteomewide, label-free DIA and DDA data processing
- If you have the hardware, Skyline should be able to use up to 100% CPU and 100% of your memory. Though we continue working on making it do more with less.
- Performance improvements in very large DIA (6,000,000 transitions x 20 files)
- Convergence detection in mProphet modeling and 10 iteration maximum (down from 30)
- New --import-process-count=[num] and --import-theads=[num] arguments for SkylineRunner. The former can yield up to 10x import performance improvement on a 24-core NUMA server and 2-4x on a standard i7.
Reduced .sky file size by 70% for large (over 1000 transitions) files
Multi-peptide peak area graph
Customizable color schemes
Import isolation scheme feature from DIA data files
Improved iRT calibration from DDA data directly into spectral libraries
Storing raw chromatograms in SKYD files. This is a big one which also gives us:
- View > Transform > Interpolated (F12) shows the chromatograms as Skyline used to show them
- View > Transform > None (Shift+F12) shows the raw uninterpolated chromatogram
- Skyline can now always show in Full-Scan graph every spectrum from which chromatograms were extracted. Previously interpolation could cause spectra to be skipped
- A new report value TransitionResults.PointsAcrossPeak
- File > Share can now create document archives in 3.6 format for sharing to Skyline 3.6
File > Export > Spectral library for exporting targeted results as a spectral library for your next experiment
Support for semi-cleavage enzymes in Peptide Settings - Digestion tab
Support for Associate Proteins checkbox in View > Spectral Libraries with background proteome for nonspecific cleavage
Run-to-run retention time correlation graph
New file details (score type, score cut-off, unique peptides and spectra) in Spectral Library Explorer source file details form.
Support BLIB files with StartTime and EndTime in the RetentionTimes table
- Allowing external tools to provide their own peak detection and picking
- Times are used for peak integration boundaries without further peak detection
- Faster imports and smaller resulting files
File > Import > Peak Boundaries 2-10x faster
Add Total Ion Current Area under Results.File in reports/Document Grid
Add "Equalize Medians" as normalization method in Peptide Settings / Quantification for large exploratory experiments where most targets are not changing
Improved paste performance in the Document Grid
Column tips and reference help in the Live Report view editor
New SkylineDailyCmd.exe in same folder as Skyline-daily.exe with same command-line interface as SkylineRunner.exe, but runs Skyline in a single process, useful for ZIP-file or Administrator installations where these EXEs are placed in easily located paths
Proteome Discoverer 2.2 support in spectral library builder
Improved support for SCIEX Midas workflow
Improved support for Agilent IMS workflow
Improved handling of importing modified peptide sequences with SCIEX 3-letter modification abbreviations
Export transition list feature for mixed polarity small molecule documents to allow exporting different polarities separately
Various other fixes such as:
- Use of .NET API to encrypt passwords for Panorama and Chorus stored by Skyline in its user.config file.
- Fix to z ion mass calculation, which was off by one hydrogen atom
- Fix to View > Mass Errors > Replicates graph to match colors with other replicate graphs when MS1 and MS/MS XICs are present
- Fix y axis scaling in chromatograms which had problems when IDs or Predicted annotations were present and scale was less than 100
- Fix tracking of changes to iRT standards to better match changes to documents
- Fix to avoid removing iRT standards when Edit > Refine > Advanced minimum transition count is higher than they contain
- Fix to keep from duplicating spectrum source files - especially problematic for iRT training - in spectral libraries when a DDA file is searched twice
- Slightly more tolerant peak grouping which allows undetected peaks to be added to the group based on chromatogram correlation over the integration boundaries.
- Fix precursor matching with SRM data in fringe case where the precursor m/z is worse, but transition matching is better
- Fix error message reporting missing required columns in File > Import > Peak Boundaries
- Fix to "Unable to sort because the IComparer.Compare() method returns inconsistent results"

This requires a manual upgrade. We hope you'll take the time to visit the Skyline installation page:

https://skyline.ms/skyline64.url

And install this latest release. It should be worth the effort.

Thanks for your coninued use, feedback and support of this project.

Brendan MacLean
Skyline Principal Developer

PATCHED: Skyline 3.6 (10493)

Tue Feb 21 20:50:26 PST 2017

Dear Skyline Users, I have just released Skyline 3.6.0.10493, a patch to the original Skyline 3.6 release with several important bug fixes and finalized Chinese and Japanese translations. Fixes include: - Fix for negative ion mode DIA (thanks to Brian) - Collision energy equations for Thermo Quantiva (provided by Sue) - Improvements in handling Waters SONAR data (thanks to Brian) - Fix for saving .sky files to folders with non-ANSI characters (thanks to Nick) - Fix retention times in Agilent IMS data (thanks to Brian) - Fix group comparison graph to respond to settings changes like confidence interval (thanks to Nick) - Fix for Agilent negative polarity data (thanks to Brian) - And a number of other unexpected exceptions (mostly thanks to Nick) Skyline should ask to update automatically after you restart twice. Thanks for using Skyline and especially thanks to all of you who have reported issues or posted exceptions when you got an unexpected exception message. --Brendan

Skyline 3.6 Released

Mon Nov 07 22:27:21 PST 2016

Dear Skyline Users,

After nearly a year of hard work from the entire Skyline team, Skyline 3.6 has just been released. This release again greatly exceeds our previous efforts, and many new people have signed up for the Skyline development release known as Skyline-daily, nearly doubling in number to 1250, and responsible for 25% of all start-ups per week. Along with many thousands of hours of automated test runs, that helps to make this the best-tested Skyline release ever, by far.

New features include:

Improved results import:
- Parallel multi-file results import (in user and command-line interfaces)
- New results import interface for improved unattended imports
- Greatly improved import performance for Skyline documents on network drives
Calibrated quantification improvements:
- Surrogate standards for normalizing to explicit non-homologous molecules
- Remove point right-click option in calibration curve graph
- Explicit Global Standard Area added to replicates for explicit global normalization control with values like TIC
Group comparison additions and fixes to improve consistency with MSstats
New Detection Q Value and Detection Z Score report columns for mProphet scored peak picking
New Peak Rank By Level report value and Targets view showing separate peak rankings for MS1 and MS/MS transitions
Peptide uniqueness constraint added to Peptide Settings - Digestion tab (by protein, gene or organism)
New Edit > Refine > Associate Proteins for adding protein associations for targeted peptides after they have been added to the targets list
Ability to choose which modifictions to use when showing a library in the Spectral Library Explorer
New and improved plots:
- Mass error plots (replicate and peptide comparisions and 1D and 2D histograms
- Multi-peptide retention time plot
- Point set selection in retention time regression plot
Improved small molecule support:
- Improved support for negative ion mode
- Improved chromatogram matching for molecules with identical precursor m/z but different scheduled retention times
- Parsing of chemical formula with adduct syntax in Edit > Insert > Transitions
- Support for small molecule transition list import with Edit > Paste, File > Import > Transition List, external tools and with command-line
Improved Transition Settings for Full-Scan
- Centroided extraction with mass error tolerance made default, based on improvement seen with Thermo, Sciex and Bruker instruments
- New high-selectivity extraction option (1/2 extraction width) for extraction from profile spectra, based on improvement seen with Termo and Sciex raw data files
- Easier import of existing data with improved isolation schemes based on raw data
- Fixed support for importing from instruments using different high- and low-resolution between MS1 and MS/MS
Ability to include ambiguously matched spectra in spectral libraries build by Skyline
Improved support for iRT:
- Support for more iRT standard mixes
- Automatic adding of iRT standard targets to document
- More flexible iRT regression support (allowing 80% of standards at 0.995 correlation)
- CiRT support
SkylineRunner command-line interface improvements:
- Command-line support for importing transition lists and assay libraries
- Command-line support for exporting isolation lists
- Command-line support for adding decoy peptides
- Improvements made to support AutoQC
- mProphet model generation output to console log
Initial support for Sciex MIDAS data
Initial support fixes for Waters SONAR data
Fix for File > Save As bug that disabled Edit > Refine > Re-import
Many other smaller bug fixes

Unfortunately, it looks like we still have issues with automatic upgrades between major releases. If you are asked to upgrade automatically after restarting twice, this upgrade will help get you to the installation page to use for upgrading manually. Otherwise, this upgrade will require going to the Skyline download page and installing over your current installation. If this does not work, please consult the Recovering From a Broken Installation page, before requesting support in upgrading.

Enjoy! And thanks again for using Skyline, providing feedback and helping us to continue improving the software.

--Brendan

PATCHED: Skyline 3.5 (9319)

Sun Jan 24 21:53:34 PST 2016

Dear Skyline Users, UPGRADE!! I have just released Skyline 3.5.0.9319 with all relevant fixes we have made since releasing Skyline 3.5: - Fix ability to use a UI language (English, Chinese or Japanese) other than the current system language - Fix clicking on labels in multi-peptide graphs (e.g. when proteins are selected in Targets view) - Fix iRT issues where iRT standards appear more than once in the document - Accept heavy/light/etc labels in a small molecule transition list without any formulas - Fix performance importing chromatograms from data on Chorus - Fix for importing data from Sciex QTRAP 4500 - Fix to use Explicit Retention Time values in peak picking, especially for small molecules - Fix excessive percent complete output from command-line interface in parallel operations - Fixes to assay library import generated with Sciex tools - Fix cases where popup windows come up on wrong monitor when using multiple monitors - Fix for most common unexpected error "An item with the same key has already been added." in "LoadLibrary" - Fix problem where "ratio to standard" would be NaN if any of the heavy transitions had zero peak area - Fix case where progress form came up behind Peptide Settings form during long Peptide Settings changes Remember, you may have to upgrade manually from the Skyline installation page: https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view If Skyline does not offer to update automatically after you restart twice. If you experience issues with a manual installation, please consult the help page on dealing with a broken installation: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install We encourage you to upgrade from earlier releases. Over 60% of all Skyline instances started are now Skyline 3.5. Especially with this patch release, we are now very confident that Skyline 3.5 is a major upgrade from prior releases. Enjoy. --Brendan

Skyline 3.5 Released

Tue Dec 01 23:39:24 PST 2015

Dear Skyline Users,

After many months of hard work from the entire Skyline team, Skyline 3.5 has just been released. There is no question that this release greatly exceeds all of our previous efforts. Word got out, and many new people have signed up for the Skyline development release known as Skyline-daily, now numbering over 750 users, responsible for over 1000 start-ups per week for the past 2 months. Along with hundreds of hours of automated test runs, that helps to make this the best tested Skyline release ever.

With all of the webinars, week-long courses (already 5 scheduled for 2016) and new tutorials, this is also the best documented and supported release of Skyline.

New features include:

Calibrated quantification (a.k.a. absolute quantification) [see tip]
Impressive performance improvements for large full-scan data sets (DIA and DDA)
Many longer operations made much faster and showing progress form allowing cancel
Chromatogram extraction from centroided scans using mass accuracy in PPM (Peptide Settings - Full-Scan tab, using Centroided mass analyzer)
Improved small molecule support:
- Support for negative polarity ions
- Support for multiple ions per precursor, including isotope labeling
SkylineRunner command-line improvements supporting processing pipelines from raw data to Panorama uploads
Improved assay library and transition list import with better modification guessing
Full support for Panorama AutoQC system suitability run processing
Support for building spectral libraries from DIA-Umpire search results
Ability to include report templates in document with Document Settings
Fill Down function available on Document Grid right-click menu
Delete-key clears cells in Document Grid
Apply to All for faster manual correction of multi-replicate peak picking
Compensation voltage optimization for Sciex instruments with SelexION
Default Sciex SWATH isolation schemes and abilitly to export Sciex isolation lists
Automated drift-time training for Agilent and Waters IMS Q-TOF instruments
Lockmass correction for Waters Q-TOF data
Export directly to instrument methods for Shimadzu QqQ instruments
Many display improvements:
- Peak area and background shading of selected transition
- New residuals plot in Retention Times > Regression graph
- Keep ID annotations from being hidden by chromatograms
- Improved dotp display in Peak Areas plot
- Option for strict scientific notation for intensity y-axis on plots
- Graph text scaling based on right-click > Properties for all graph text

Unfortunately, it looks like this upgrade will require going to the Skyline download page and installing over your current installation. If this does not work, please consult the Recovering From a Broken Installation page, before requesting support in upgrading.

You definitely want to make this upgrade, though. This one is worth it.

--Brendan

PATCHED: Skyline 3.1 (7382)

Mon Apr 13 08:50:15 PDT 2015

Dear Skyline Users, I have just released Skyline 3.1.0.7382 with a number of important fixes for Skyline 3.1: - Fixed issue with saving small molecule documents with precursor isotope distributions - Fixed spectral library build support for Waters final_fragment.csv files with IMS drift times - Fixed method export of unscheduled PRM and DIA for Bruker TOF instruments - Fixed issue where quick filters were not applied when grids were exported or copied - Fixed unexpected error trying to calculate peak scoring model with DIA isolation schemes that included a target column - Fixed unexpected errors in group comparison interface - Error handling when importing results from Chorus If you have upgraded to version 3.1, Skyline should offer to upgrade automatically after you restart twice. If you have not yet upgraded to 3.1 (and you are not running Windows XP), please do so now! There are many improvements and bug fixes in version 3.1 from 2.6. This does require a manual upgrade. Just go to the appropriate installation page, and install 3.1 over your existing Skyline version. You should not need to uninstall. If you run into any issues attempting to upgrade, please consult the following page for troubleshooting help: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install Thanks for using Skyline in your research! --Brendan

PATCHED: Skyline 3.1

Mon Mar 16 21:55:29 PDT 2015

Dear Skyline Users, Sadly, one of our final attempts to fix a window activation issue in Skyline went awry, leaving it impossible to dock a number of windows (Document Grid, Results Grid and Group Comparison windows). They would just disappear when you tried. This has been fixed with a patch release, Skyline 3.1.0.7316. If you have already successfully upgraded to 3.1, then Skyline should ask you to upgrade again automatically after you restart twice. If you have not upgraded, then you still need to upgrade manually and this should have little impact on you. Apologies for the inconvenience, but you really want this fix. --Brendan

Skyline 3.1 Released

Mon Mar 16 07:59:15 PDT 2015

Dear Skyline Users,

I have just released Skyline 3.1.0.7312, the most recent update to the Skyline public release.

First, in updating to this release there are two things you should be aware of:

This release no longer supports Windows XP (nearly 1 year after Microsoft stopped supporting it).
Upgrading requires that you go to the Skyline web page and install again manually. (NO AUTOMATIC UPGRADE)

PLEASE UPGRADE!! And you will get the following improvements:

Integrated Group Comparison support (see images below). Get started with:
- View > Group Comparisons > Add
- Settings > Document Settings - Group Comparisons tab
- Tutorial coming soon...
Support for custom ions / small molecule targeted MS
- Use Edit > Insert > Transitions - Small molecules to start a Skyline small molecule document
- Watch Skyline Tutorial Webinar #4 - Preview of Small Molecule Support
Cloud chromatogram extraction from full-scan data with Chorus
- Consult the Chorus Cloud Chromatogram Extraction tip to get started.
New wizards for importing peptide searches with PRM and DIA data sets
Direct filtering of Document Grid views
Support for iRT scores in chromatogram libraries from Panorama
Faster start-up and file open and save progress
Fully enforced light-heavy ion matching and Find form support for "Mismatched transitions"
Improved optimization library support
First draft translations for Chinese and Japanese

If you experience trouble upgrading to this version, please check the following page before requesting support:

Recovering From a Broken Installation

Thanks for using Skyline in your research.

Brendan MacLean
Skyline Principal Developer

Skyline 2.6 Patched II

Sun Feb 08 12:17:57 PST 2015

Dear Skyline Users, I have just released Skyline 2.6.0.7176 with fixes for just a few issues found since the first patch. These include: - Unexpected error building a spectral library from ProteinPilot .group files - Unexpected error importing results into a .sky file located in the root folder of a drive - Issue where manual integration was lost in labeled experiments when "Synchronize isotope label types" checkbox was used - Fix modification shortname export for Sciex transition lists with explicit and variable modifications If you haven't updated to v2.6 yet (about 10%), you really should. You'll see a lot of improvement over prior releases, and very few issues are now being reported. Skyline should ask you to update automatically, after you restart twice. If it does not, please follow the advice on this page before posting to the support board for help updating: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install Thank you for using Skyline in your research. Brendan MacLean\\ Skyline Principal Developer

Skyline 2.6 Patched

Mon Oct 27 05:56:23 PDT 2014

Dear Skyline Users, I have just released Skyline 2.6.0.6851 with fixes for a number of bugs found in the original Skyline 2.6 release. These include: - Fix to open without error Panorama published and File > Share - Minimized files with newer spectral libraries - Fix Mascot library building threshold to use homology score instead of identity score (recommended by John Cottrell) - Fix isotope distributions for 18O labeling - Fix most common unhandled exception in chromatogram graph - Fix chromatogram graph full-scan tracking dot not showing up with Split Graph on MS1-only data - Fix unhandled exception in Peptide Settings validation of spectral library IMS resolving power - Fix changing DIA isolation scheme not updating peptides with all precursors removed - Fix Import Peptide Search wizard removing to much when remove prefix option is chosen - Catch errors in Start page and Tool Store when no internet connection - Better tie-breaking for q values in MSF files If you haven't updated to v2.6 yet (about 23%), you really should. You'll see a lot of improvement over prior releases. Skyline should ask you to update automatically, after you restart twice. If it does not, please follow the advice on this page before posting to the support board for help updating: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install Thank you for using Skyline in your research. Brendan MacLean Skyline Project Lead

Skyline 2.6 Released

Mon Sep 22 09:12:14 PDT 2014

Dear Skyline Users,

I have just released Skyline 2.6, with many exciting new features, improved workflows and better peak picking.

This release includes the following improvements:

Full-Scan spectrum view for chromatograms extracted from full-scan data, with heat-map graph for IMS data
- If you are using chromatogram extraction workflows (MS1 filtering, PRM, DIA), then you really want this
New Skyline start page for faster access to common starting scenarios and tutorials
Ion mobility drift time filtering for Agilent and Waters TOF instruments
Optimization library support for storing optimized CE values
Custom fragment ion support for defining non-peptide-backbone fragments (like iTRAQ, TMT, etc.)
Support for isotope labeling experiments (like SILAC) without standards
Support for Shimadzu triple-quadrupole instruments
Improved chromatogram peak picking
Import of tabular "assay library" format
Support for protein details information (accession number, gene name and preferred name) queried from internet sites
DIA isolation scheme viewer
Option to exclude transitions within the DIA isolation window for the precursor
First draft translations for Chinese and Japanese, with more translated than in 2.5

Skyline should ask you to update automatically after you restart twice. If not, please check the following page before requesting support:

Recovering From a Broken Installation

Thanks for using Skyline in your research.

Brendan MacLean
Skyline Project Lead

Skyline v2.5 Patched and Open Registration for Skyline-daily

Thu Jul 10 15:37:57 PDT 2014

Dear Skyline Users, I have just released Skyline v2.5.0.6157, which adds only a fix to the most commonly reported unexpected error message: ArgumentOutOfRangeException, SettingsListBoxDriver.cs:line 58 We have been getting several of these every day since the last patch release (2.5.0.6079). My apologies for taking so long to fix this. The Skyline team has been extremely busy creating Skyline v2.6, which is now feature complete, and due out later this summer. To allow more people access to the latest features as they are developed and get more people testing them, I have decided to open registration for the Skyline-daily release to all registered Skyline users (that includes you). If you are interested in beta-testing the newest features described on this page: https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view?pageId=Release%20Notes Then register for Skyline-daily on this page: https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/daily/register-form/begin.view Skyline-daily can be run on the same computer with the normal public release of Skyline, though it has a different file format, which means files saved in it cannot be opened in the public release. Skyline-daily can, of course, open files saved from any prior releases. Thanks for using Skyline in your research and helping to make it grow with your needs. --Brendan

Skyline v2.5 Patched, with Chinese and Japanese Translations

Mon May 05 16:17:04 PDT 2014

Dear Skyline Users: I have just released a patch to Skyline version 2.5 (with the version number 2.5.0.6079). This release includes a first draft of the user interface translated to Chinese (Simplified) and Japanese (if you have appropriate system settings, or you use Tools > Options - Language to set the UI language). There are also versions of the Targeted Method Editing tutorial translated to these languages: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_method_edit_zh\\ https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_method_edit_ja This is a first attempt, and we know that there are a few things that we were not able to translate this round (most notably, the column headers for Skyline reports), but we expect to have these fixed for the Skyline summer release later this year. We are also now working on translating more tutorials, in this continuing effort to make Skyline more accessible to its growing worldwide user community. Thanks very much to the people who made this possible with the time they put into reviewing and revising the work of the companies that produced these translations. Chinese - Chaochao Wu, ChenWei Lin, Ping Yan, Tao Liu, Yansheng Liu, Yibo Wu\\ Japanese - Fumio Matsuda, Itaru Samejima, Katzutak Shimbo, Kiriko Matsuo, Sayaka Shibata, Xiaoshan Yue, Yasushi Ishihama And the instrument vendors whose funding of the Skyline project made the translation possible: Agilent, Bruker, Shimadzu, Thermo, Waters This release also contains the following bug fixes applied to version 2.5: - Fix Import Results to write temporary files to document directory instead of raw data directory to allow importing from read-only network drives - Fix for demultiplexing of MSX data with overlapping windows - Improved library building from MSF files - Fixed a number of unexpected error cases Skyline should ask you to update (from 2.5.0.5675) automatically, after you restart twice. If it does not, please follow the advice on this page before posting to the support board for help updating: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install Thanks for using Skyline in your research. I look forward to meeting many of you soon at the Skyline User Group Meeting at ASMS. Brendan MacLean\\ Skyline Project Lead

Skyline v2.5 Released!

Sat Feb 08 20:13:54 PST 2014

Dear Skyline Users: Only 5 months after releasing v2.1, I am extremely excited to announce the release of Skyline v2.5. As the numbering indicates, this is a big jump for such a short release cycle. This is because we are releasing advances in two major areas that have been under development, but not yet released, for over a year: - Live Reports - mProphet/OpenSWATH integration We haven't stopped working on these areas, but you will be seeing years of development time in this release. The full feature set added in v2.5 includes: - Live Reports - interact directly with Skyline documents through a grid interface with -- Customizable column display -- Sort and filter -- Direct paste to annotation values -- Text search -- Much faster report generation than the original Custom Reports - Improved peak scoring and picking -- Improved default peak picking -- Integrated mProphet and OpenSWATH scores and semi-supervised learning model training -- Edit > Refine > Reintegrate form for applying non-default peak scoring and picking models -- Peak q value assignment -- Model training and evaluation interface - Global standard type assignment -- Right-click > Set Standard Type to assign Normalization and QC standard types -- New icons to display iRT, Normalization and QC standard types in Targets view -- New ratio values for peptides, precursors and transitions to global standard types in Peak Areas graph and reports -- All global standard peptides measured in every method of multiple method documents - Fully integrated Tool Store user interface -- Tools > Tool Store form for reviewing and installing External Tools without leaving Skyline or manually downloading files -- Update notifications for new tool releases -- Tools > Updates form for automatic updates to installed tools - Multi-peptide chromatogram graphs - use protein selection or multiple selection (shift- or ctrl-click) to see annotated chromatogram peaks for many peptides at once - Improved support for Scheduled Extraction of chromatograms from full-scan mass spectra - Improved File > Import > Peptide Search wizard - Thermo raw file import support on systems with European number format settings To help you get up to speed on these latest advances, we have written a new peak picking tutorial and majorly revised three other tutorials (MS1 Full-Scan Filtering, Targeted MS/MS, Custom and Live Reports), which you can find here: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorials If you are using a recent public release (i.e. v2.1 or v1.4), then Skyline should ask you to upgrade automatically after you restart twice. If it does not, please consult the following web page before you post a support request: https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install Thanks for using Skyline in your research. I look forward to meeting many more of you this year at the courses and conferences where Skyline and targeted proteomics will be taught and discussed. Brendan MacLean\\ Skyline Project Lead

Support for Windows XP Ending

Wed Dec 11 16:02:55 PST 2013

Dear Skyline Users, This is just a quick note to warn you that sometime in 2014, Skyline (following the lead of Microsoft http://windows.microsoft.com/en-us/windows/end-support-help) will end its support for Windows XP. If you are dead set on sticking with an operating system that was first released over 12 years ago, which hasn't seen a major service pack in over 5 years, and which soon won't even be supported by Microsoft, you may also not care that Skyline will continue forward sometime in 2014 without you. You will still be able to use the last Skyline release to support Windows XP for the next 12 years (without support), but you won't be able to upgrade to new releases and expect them to work on Windows XP. I will be very clear about when this actually happens, and it won't happen before our next public release, but probably the first public release after Microsoft itself discontinues support, and earlier for the Skyline-daily development release. Thought I would give people on Windows XP some lead time while 2014 budgets may not yet be fixed in stone, and holiday gift lists have not all been filled. Time to think about upgrading. --Brendan

Skyline v2.1 Released!

Sun Sep 08 22:39:26 PDT 2013

Dear Skyline Users:

After nearly 10 months of hard work by a growing and vibrant team of software developers and scientific collaborators, with a lot of great feedback from many of you, I am proud to announce that Skyline v2.1 has been released.

Two of the most exciting developments in the past year have been integrating new supporting tools around Skyline:

Panorama Targeted Proteomics Knowledge Base - a data base web site for sharing, storing and reviewing collections of Skyline documents, and for creating Chromatogram Libraries from empirically measured targeted data.
External Tools - a new collection of external statistical tools directly integrated into Skyline with automated installation support, including MSstats for grouped studies and QuaSAR for response curves, LOD/LOQ and AuDIT interference analysis, and hopefully many more to come. Download the ZIP files and follow the tutorials to get started.

Other new features include:

File > Import > Peptide Search wizard for DDA data quick start
Mass accuracy metrics for high resolution full-scan data
TIC and base peak chromatograms from MS1 survey scans
Installed support for Bruker TOF data, with improved performance
Demultiplexing of overlapped DIA/SWATH methods
Direct pasting into the Results Grid (especially useful for replicate annotations for external tools)
Fix to be able to distinguish peptides with the same precursor m/z in MS1 filtered data
Improved memory performance for large full-scan imports
Enhanced results data import progress interface with peak graph
Split chromatogram graphs for simultaneous viewing of light and heavy transitions, and precursor and product ions
Alignment by iRT scores in graphs
Improved integration with PanoramaWeb
Save and restore of Targets View expansion and selection state
Several spectral library builder fixes, including support for larger libraries and pepXML/mzXML from PEAKS
File > Import > Peak Boundaries for importing peak selection from other tools
File > Export > Chromatograms for exporting chromatogram points
Bug fixes too numerous to count

If you are using a recent public release (e.g. v1.4 or v1.3), then Skyline should ask you to upgrade automatically after you restart twice. If it does not, please consult the following web page before you post a support request:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tip_recover_install

Thanks for using Skyline in your research. This really would not be possible without all of you.

Brendan MacLean
Skyline Project Lead