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Joseph Brown, Ph.D.

  Joseph Brown, Ph.D., is a senior scientist in the Biological Sciences Division at the Pacific Northwest National Laboratories. His work focuses on using high-throughput “-omic” technologies to investigate the global response to pathogenic viral infections within humans and nonhuman primates. Joseph earned a BS in molecular biology at the University of West Florida. In 2002, he joined the...

Std curve

Hello, I would like to set up a standard curve in Skyline but not sure where to input the concentration values of my std runs as well as set the sample type to standard, see attached? Hi Stoyan, Your best resource would be the webinar on Calibrated Quantification with Skyline: http://skyline.ms/webinar13.url Hopefully, it is laid out pretty clearly there. We also have an updated tutorial...

MSstats DIA error

HI I’m using Skyline daily 2.4.9.56.16 on windows 7 I've successfully replicated the tutorial data treatment But when I try to run MSstat on my DIA data from Skyline I get an error about missing value (see txt file) I checked "integrate all" in order to always have a peak selected in Skyline but nothing changed. To which missing value does it refer? In the ppt I pasted some screenshot of the...

Reports / stats tools

Hi Brendan, I look forward to the second webinar (DIA workflow) and have a suggestion regarding a future webinar. It would be nice to focus a webinar on how to generate maximally informative reports with Skyline and the external tools such as MSStats, MS1Probe, and PopulationVariation. A question related to that topic: How do you best assign and organize annotations (treatment group, whether...

Results import

Hi Brendan, When importing MRM results I only see options for replicate analysis i.e. software treats all imported runs as replicates. However, what if one wants to import non-replicates i.e. different concentrations, treatment days etc? Stoyan Hi Stoyan, I needed a single term to apply to everything, and I chose "replicate". In Skyline parlance, "replicate" means a set of mass spec runs...

MS1 extraction

Hi Brendan, I am trying to use the MS1 estraction application in Skyline. So far it is working but now that I want to add some peptides to my list I can not get chromatographic information (see attached file). I also woul like to know how to introduce a modification in the N-terminal of the peptide. When I use the option "modify" it only allows me to modify the residues but not the N-terminal terminus....

618 : Problem accessing MS/MS in method with multiple fragmentation modes

closed
2018-12-22
2019-02-15
Moving this request from support to the issues list to avoid losing it. Please add your insights, Matt.

I uploaded a BSA digest we run in PRM that includes several modes of fragmentation and is not supported by Skyline at the moment. We use this for our QC of the Lumos and fragment using CID, HCD and ETD. At the moment we can only see the MS1 signal in Skyline, but not the MS2, which we would very much like to.
The file name is FS1LC2_BSA_HCD-IT_28082018_01.raw

https://skyline.ms/announcements/home/support/thread.view?rowId=32997
I'm not seeing any problem reading that file from a ProteoWizard perspective. Loads fine in SeeMS and converts in MSConvertGUI and I can see all the expected activation types. You want me to look into it in Skyline? I suspect it's breaking a heuristic somewhere.
Yes. Please try to reproduce it in Skyline and see what you can come up with. If you don't feel comfortable proposing the fix, then hand off to Nick or Brian Pratt.
On the support thread we decided the current workaround with pre-filtering the file into pseudo-replicates for each activation type was sufficient for now given that this is a very rare use case (although the less rare ETD/CID or ETD/HCD would require similar treatment, so if that gets more common we may revisit this).

Clustered Report values doesn't match with manual calculation

Hi, I performed a simple group comparison between the control and treatment groups at the protein level, which generated a table showing fold changes and adjusted p-values. While cross-checking the values from the Clustered Report against those I manually calculated from the Document Grid, I noticed they don’t match. I’m certain I’m missing something in the process, but haven’t been able to pinpoint...

Adam Officer

  Adam Officer is currently a Research Associate at the Broad Institute of MIT and Harvard in the Proteomics Platform working under Dr. Jacob Jaffe. His research is based around the Library of Integrated Network-Based Cellular Signatures Program and aims to apply high-throughput proteomics to create a database of targeted proteomics signatures to ask questions that deepen our understanding...

Normalizing Unknowns?

Hello: I am running a peptide quant experiment and spiked the same amount of ISTD into each unknown. . However, according to the BCA assay, a few of the unknowns had a very small amount of protein (likely due to treatment) so I was unable to inject the same amount of total protein for each sample. Is there a way to normalize these small amounts (i.e. I injected 10x less material for unknown 1...

Ellen Casavant

  Ellen Casavant, Ph.D., is a Senior Scientist in the Biomarker Mass Spectrometry team within the department of Translational Medicine (TM) at Genentech. The biomarker mass spectrometry team aims to develop mass spectrometry data acquisition methods and analytical techniques to support measurement of clinically relevant candidate biomarkers from large clinical cohorts to help inform drug development...

Live Report > Group Comparison

Hi, I performed a simple group comparison between the control and treatment groups at the protein level, which generated a table showing fold changes and adjusted p-values. Is there a way to quickly extract the actual intensity or abundance or ratio values that were used behind the scenes to calculate these results? Our collaborator would like to have these values in Excel format to cross-verify...

Problems with peak scoring and export of DIA-data

Dear Skyline team, thanks for developing skyline and your consistent support. I use Skyline (version 4.1.0.18169, 64-bit) for analyzing a DIA data set of 15 .raw files (Thermo) by a library of 300 .raw files (both samples and library ran with iRT's). The settings I used are pretty much the same as they are recommended in the two DIA-Webinars. For my analysis, I have adjusted the iRT and used shuffled...

914 : Proteomics features still showing in small molecule mode

closed
2022-10-18
2023-05-03
During the latest iteration of Skyline-Online for small molecules, the following proteomics features were found to show up when Skyline is in small molecule UI mode:
1. Reports that no longer show up in the Document Grid - Reports (Peptide Quantification, Peptide Ratio Results, Peptide RT Results, etc.) show up in the list under File > Export > Report. If you click the "Edit list..." button in this form, you see a list with certain items grayed out. I think the grayed out items should no appear in the "Report:" list under File > Export > Report. Possibly, we should categorize tools by whether they are small molecule or proteomics tools and hide/show their reports based on this.
2. In the Molecule Settings - Library tab, clicking the "Build..." button shows a form with "Data source" for "Files" and "Prosit", but Prosit is a Proteomics-only tool. So, the small molecule form probably should have the "Data source" box hidden, and controls below it shifted up to its y-position.
3. If you give your library a name in the Build Library wizard and then click the "Add Files..." button, the file types drop-down list contains "Matched Peptides" and a very extensive list of peptide spectrum matching tools that produce output formats we recognize for library building. This should be changed to "Matched Molecules (*.ssl)" (adding any other output formats that we know we support for small molecules.
fixed 5/1/2023 in commit 9c54301acc504061035e09f4924d5c3e10f31a82

* fixes for Issue 914: "Proteomics features still showing in small molecule mode" (#2577)

* The Prosit-related controls in the Build Library dialog should not appear when the UI is in small molecule mode

* Tooltips for menu items weren't being processed for ModeUI peptide->molecule treatment

* Make the Build Library dialog file picker ModeUI aware - don't offer proteomic-only file .ext selections

* restrict the reports offered in File > Export > Report to those that make sense in the current UI mode, using the same technique as in the Document Grid

reported by Brendan

Emily Crawford

  Emily Crawford completed her B.S. in Chemistry in 2023 at the Georgia Institute of Technology in Atlanta, GA. She is currently an analytical chemistry Ph.D. candidate at the University of North Carolina at Chapel Hill in Dr. Erin Baker’s laboratory. Here, her research focuses on optimizing separation and mass spectrometry techniques to assess the effects of pharmaceutical pollution on...

"1-s2.0-S1570023217301642-main.pdf" attached to message "is there possible to improve modification types of skyline?"

Contents lists available at ScienceDirect Journal of Chromatography B journal homepage: www.elsevier.com/locate/jchromb The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures Caroline Bayarta,b, Sébastien Peroninc, Elisa Jeanb, Joseph Paladinob, Philippe Talagad, Marc Le Borgnea,⁎ a Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie...

Elena Barletta

  Elena Barletta holds a bachelor degree in biology from the University of Rome “Tor Vergata” (Italy) and a master degree in biology from the University of Geneva (Switzerland). During her master degree study at the University of Geneva and the Swiss Institute of Bioinformatics (SIB), her project was focused on the analysis and interpretation of proteomics data, mainly of mass-spectrometry....

Background correction inquiry

Hi Brendan,   I'm really impressed with your background correction feature. I avoided moving analysis of a project to skyline since the controls were so noisy (after treatments the signal went sky high though) but I recently did since i wanted to re-analyze my entire dataset for consistency and my manually integrated data is a lot like the skyline results. Well done! However, I was wondering...

problems locating skyline installation in windows server 2012 R2

Dear skyline support, I have a running installation of skyline and skyline daily on windows server 2012 R2. But skyline is not displayed in the list of installed apps, nor can I find on my system when using the search tool. I suspect this has something to do with the roaming user profiles used. As soon as I right click on a skyline doc, skyline opens up, so it is def. there and functional. Is there...

2024-05 Doud.pdf

“Fit-for-purpose” targeted mass spectrometry for quantification of chimeric Aducanumab CENTER FOR PROTEOME ANALYSIS, INDIANA UNIVERSITY SCHOOL OF MEDICINE Skyline User Meeting, ASMS 2024 Emma Doud, Ph.D. INDIANA UNIVERSITY 1.Background 2.Study Design 3.Assay Design 4.PRM implementation Alzheimer’s Disease and MODEL-AD INDIANA UNIVERSITY  ~50 million patients worldwide  By 2030:...