Table of Contents
I followed the Isotope label presentation and configured the peptide and transition setting. This product (TMT10Plex) has been used and seemed to be the same as Skyline pre-set. https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0016969_2162457_TMT10plex_UG.pdf&title=VXNlciBHdWlkZTogVE1UMTBwbGV4IE1hc3MgVGFnIExhYmVsaW5nIEtpdHMgYW5kIFJlYWdlbnRz
So I did the two steps that demonstrated in following documents in pages 75 and 76 of the Chemical labeling section as follow:
Yet, I see no TMT transitions under precursors.
Any suggestion as what went wrong?
I really appreciate your help.
Dear Skyline Team,
I would like to perform de-isotoping on my direct infusion lipidomics data from a triple quad MRM experiment. While just performing a correction for M+2 isotopic overlaps based on theoretic abundance of 13C would be straigtforward, the additional effect of distribution of heavy carbons in the detected fragment in Q3 makes the calculation quite a bit more complex. Could I use skyline to perform this de-isotoping routine? Are there any other tools that you could recommend?
Thank you very much in advance for your advice. Best wishes, Thomas
Hi Skyline Team,
I would like to ask you to answer my questions please.
1) In the Proteome Discoverer, I uploaded raw data from MS, divided into three types and from these three types I created three libraries – each type had its own library. Is there any difference to upload all three libraries into Skyline, in which I evaluate the data of PRM analysis, or to upload them as one common library?
2) We did targeted analysis on MS and the samples were measured in triplicates. Is it better, during the process of evaluation in Skyline, to do the average (total ratio) of all three replicates or just to select the most suitable replicate?
I would like to install older versions of Skyline, but I can not find any download links. Is it still possible to get them?
When I tried install Skyline 20.2, occurred error installing .NET Framework 4.72 (attached error massage).
My company laptop runs an older version of Windows 10 (build 10240) which I'm unable to upgrade.
Since this version does not support .NET Framework 4.72, I would like to install an older version of Skyline on my computer.
Is there a link for installation of older version of Skyline versions in your web site?
I'm new to Skyline and trying to take advantage of Skyline's new capabilities to analyse crosslinked MS data. I crosslinked two proteins with DSS and added DSS as a modification in Settings>Peptide Settings>Modification>Edit modifications dialogue, also ticking the crosslinker box. However, if I select it as a modification and then import a FASTA file of my proteins, the crosslinked peptides do not show up as a potential entry. When I check the Modifications dialogue again, the box has been unchecked. I've noticed the box does not get unchecked if the crosslinker box is not checked.
Did i add the modification in the wrong place? Additionally, does Skyline produce all the potentially crosslinked peptide pairs like it produces peptides digested by Trypsin or do I need to provide that list?
Our IT team has asked if silent-mode installation is supported for Skyline / Skyline Daily to suppress installation dialog and progress indicators. This approach is their preferred practice/policy and is causing some pushback.
OS = Win10, current versions of Skyline and Skyline Daily.
Gary & Kristin
Welcome to the Skyline support forum. If you have a question about using Skyline, or if you encounter a problem, you can post your questions here.
It is likely that your question has already been asked and answered. Please use the search box in the upper right corner of this screen before posting a new question.
Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community is now quite large.
If your question is about an External Tool, please contact that tool's developers directly. Contact information can usually be found on Skyline's Tools | Tool Store... menu.
When you post a question, please include the following information:
If you are including text output from a tool, please attach files to your message, rather than pasting in long text.
If you are including a Skyline document, please use Skyline's File | Share menu item (choose "Complete" if asked), which prepares a single zip file with your document and all the needed supporting files in it. Then upload that .sky.zip file to the Uploads page. If the actual raw data files are needed to illustrate a problem, those will need to be zipped up and uploaded separately.
Hi Skyline team,
I am using Skyline to analyze DDA samples by MS1 filtering. In order to increase the depth of our analysis we use HPLC to fractionate our samples prior to MS analysis. Fractions run separately on Thermo instruments (Orbi-Orbi) and we, then, perform data search using Peaks. We are also spiking our samples with labelled peptides that we are interested in quantifying.
I am having troubles applying the spectral library I built using the .pep files generated by Peaks. Whenever I select the library in the peptide settings of my skyline document data disappear. If I do not tick the library box then I can see my data. I am using Skyline (64-bit) 22.214.171.12417.
In my Peaks file there are no spectral matches for the labelled peptides as the modifications are not added during the search.
Any help would be very much appreciated.
Dear Skyline Team,
I would like to ask for your help in the following matter: I am working with proteomics, using Skyline 64-bit 126.96.36.19996. When I analyzed my data (after peak picking) I saved my Skyline datashet and closed it. After opening, it seems that the analysis (specifically my peak picking is lost/changed-please see the attached ppt). I tried to analyze the datashet in a different computer and also the option save as, instead of simple save but the same thing happens. Also, I opened some older datashets and the files seem ok (the analysis is not messed-up).
Maybe you could provide some help?
Thanks a lot,
I have done some APEX proximity labeling experiments in which I enrich for Y-biotin phenol sites using anti biotin. I would now like to build a spectral library to perform targeted quantification of these sites. I have searched the data with MaxQuant and tried importing the peptide search as usually done, but it is not recognizing the Y-biotin phenol modified peptides in my msms.txt file and these are being excluded from the spectral library. I have added the Y-biotin phenol modification to the list of modification in the peptides settings. Is there some text from the msms.txt and skyline settings that needs to match in a certain way for these peptides to be imported properly?
I am using a Thermo Exploris 480 running on Xcalibur 4.2.47. I want to import a staggered DIA method from Skyline-Daily. In method editor, after selecting DIA, import the .csv file, an error message columns don't match- The columns(s) [305.888916] from the data file are missing in the table. Do you want to proceed without importing them? Is there a way aroung this error?
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What does the red question mark mean in the chromatogram window in Skyline (64-bit 188.8.131.52)? It does not show up when clicked on the peptide or precursor m/z, but only shows up when clicked on the product m/z. Image is attached.
Hi Skyline team,
There was this post from 2013 about picking MS1 peaks based on their isotope dot-product value. Basically, I want to define an isotope distribution and if it doesn't meet the criteria, then Skyline won't allow it to be picked. Here's the post from before that suggested that this was not something that i could do, but it was in 2013 and I know you guys are updating Skyline all the time. Has this feature been implemented? This is more for a PK/bioanalysis type of measurement rather than for proteomics at all, so the data acquisition and analysis needs are different, but I thought that I'd ask.
Hello all. I have performed a calibration curve and I am trying to use QUASAR in order to calculate LOD and LLOQ. I have filled all the fields for the QUASAR input file (as I have previously done for other experiments), but it is giving me the next error:
Attaching package: 'gplots'
The following object is masked from 'package:stats':
 Processing arguments ...
 >>> Processing part 1 of 1
 Initializing ...
Error in calculate(data.subset, concentrationFile, output.prefix = outputPrefix, :
Duplicate transitions found -- try including neutral loss
Calls: tryCatch -> tryCatchList -> parse.cmdline -> calculate
I think it started happening since I last updated the Skyline daily software. Could that be the reason?
Thanks for your help.
Hello Skyline team, I am a brand new user. I went through your Method Edit/Refine tutorials. I was trying to import some Thermo Q Exactive raw files. I created a Background Proteome using a protein name of interest from the Uniprot mouse fasta file (hopefully that is the right thing to do). I would like to view the cysteine modifications of this specific protein. The Skyline error said "You must add at least one target transition before importing results." I went to Transition Settings to see what I could click on but it did not seem to help. I am using Skyline 64-bit, 184.108.40.206 on Windows 10. Thank you.
I am getting following error in all the Skylines software that I use. I am requesting suggestion for that.
Here is the error message.
At 3:31 PM:
To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.
Exception type: pwiz.Skyline.Model.Results.NoFullScanFilteringException
Error message: To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.
To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.
at pwiz.Skyline.Model.Results.SpectraChromDataProvider..ctor(MsDataFileImpl dataFile, ChromFileInfo fileInfo, SrmDocument document, IRetentionTimePredictor retentionTimePredictor, String cachePath, IProgressStatus status, Int32 startPercent, Int32 endPercent, IProgressMonitor loader) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 92
at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateSpectraChromProvider(MsDataFileImpl dataFile, ChromFileInfo fileInfo) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1263
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 249
Hi Skyline team,
I am trying to build a spectral library from Peptide Shaker output. I have test PeptideShaker 2.0.14, 2.0.16 and 2.0.18 with the same error. I tried both my search result or the example packaged with PeptideShaker. The Skyline version I am using is Skyline (64-bit) 220.127.116.113 (a7a9e8c4f).
The error message is,
System.IO.IOException: ERROR: No spectra were found for the new library.
Command-line: C:\Users\ht\AppData\Local\Apps\2.0\8MPRNX2K.0X7\9EA9LC5J.M7P\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0.99 -i testShakerOut -K -S "C:\Users\ht\AppData\Local\Temp\tmp5FE4.tmp" "C:\Users\ht\Desktop\MS_tools\PeptideShaker-2.0.16\resources\example_dataset\data\testShakerOut.redundant.blib"
Working directory: C:\Users\ht\Desktop\MS_tools\PeptideShaker-2.0.16\resources\example_dataset\data
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 156
To reproduce the error, the mzid was generated using PeptideShaker 2.0.16 -> Open Example -> Export -> Follow Up Analysis -> Skyline Export - Export as mzid -> save to "PeptideShaker-2.0.16\resources\example_dataset\data\", files of type set to mzIdentML v1.1
What can I do to solve this problem?
Great tool! I was hoping you could explain an issue I am having.
I have imported K602 and R604 SILAC labeled data and have confident library assignments for my target peptides (green circles). For K602 labeled peptides there is a total ratio provided after the dot product. However, this information is not provided next to R604 labeled peptides. Peptide settings -> Modifications have been set up so that a 'HeavyR' Isotope label type is associated with the 'Label: 13C(6) 15N(4) (C-term R)' Isotope modification and accordingly for 'HeavyK' and 'nolabel' isotope label types. Please let me know if there is anything else that I can provide.
p.s. Does total ratio refer to the light/heavy ratio?
I export a transition list from a skyline file with retention time. The RT exported are different from I saw in the library. How do I change settings to get the experiemtal RT exported? Thank you.
I was wondering if Skyline supports external calibration curves in which you inject different concentrations of heavy peptide and you use the light peptide (at fixed concentration) to normalize.
Dear Skyline team,
thanks for developing skyline and your consistent support. I use Skyline (version 18.104.22.16869, 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 decoys implemented in skyline, then I tried to improve the peak scoring by using mProphet.
However, in the outcome not all options are available (see the figure attached) that may can lead to an improvement of the peak scoring.
And secondly, I experienced while exporting protein list following group comparison that the proteinlists varies a lot between different treatments (from 10.500 down to 500). Is there any default filtering criteria (hidden) which reduces the number of exported protein lists within one analysis file?
Thank you for your comments and suggestions. I would be happy to help you out if this is necessary!
I would like to use Skyline(64-bit, 22.214.171.12469) for quantitative
proteomic analysis. I have managed to create a spectral library
already several times, but now I am unable. I use ProteinProspector
for DDA database search and generated pep.xml files, but the Skyline
said: "ERROR: 180802_03.pep.xml(line452): The .pep.xml file is not
from one of the recognized sources".
Could you suggest what should I change?
I attach the pep.xml file.
Thanks for your help in advance,
We've been working on a QC analysis of several BSA DDA runs performed on an Orbitrap Fusion. When we export the MSStatsQC report document from Skyline, we find that it lacks the "Acquired Time" data. We tried exporting the report from a single run, and it still doesn't work. We've attached the Skyline documents. Could you take a look?
Dear Skyline Team,
I would like to do DDA with MS1filtering in order to quantify a certain yeast peptide (TGAPNNGQYGADNGNPNGER) which is present in charge 2+ and 3+ with either dimethyl light or dimethyl heavy label in my dataset. I set the respective modifications in the Peptides settings tab and when I import my fasta file (which also contains some high abundant peptides to allow for matching between runs) I can see the expected m/z values present in my msms.txt (generated from MaxQuant Version 126.96.36.199). However when I next do the "import peptide search" all peptides vanish from the left side tab. When I go on I get the error message "The document does not contain any peptides". When I then try to add the Fasta file (again) I get the error message "The document must contain at least one precursor transition in order to proceed". After reading some of the earlier support threads I put the modifications.xml file from MaxQuant in the same folder (along with msms.txt and mqpar and Raw Files). I also tried the import replacing the Skyline names by the respective MaxQuant names, i.e. "DimethylLys0" instead of "Dimethyl (N-term)" in the peptide settings in Skyline. Still, Skyline somehow does not recognize the dimethyl modification from the msms.txt. When I try the import with default settings, Skyline suggests that there is Dimethl (K) my data and also an unkown K modification with the mass of 34.0 which corresponds to the heavy Dimethyl (K), but when I add them, I still get no transitions (but of course the respective N-terminal modifications are missing). When I try the import with just the Dimethyl (K) and Dimethyl (N-term) set as variable modifications (no heavy label), Skyline starts the import, however the peptide I am interested in is then only present as in the non-modified version. I tried all this with both the Skyline version 188.8.131.5219 and the Skyline version 184.108.40.206796. I would also like to add that the double dimethyl labelling settings I tried out now have worked before for another double dimethyl labelling dataset, which was also searched with the MaxQuant Version 220.127.116.11 but searched against a Trypanosoma database. I attach my msms.txt, mqpar and skys file in the hope that you can find out where the error is.
Dear Skyline Team,
I have found a workaround for my problem. I set both the light and the heavy dimethyl as structural, variable modifications. During the "Import peptide search" Skyline suggested that there is an unknown modification with the mass of 34.0 on each amino acid. I then added the heavy modifications on K and Nterm (giving them a different name) additionally as heavy modifications (mass shift of 6). The import started and I now get my peptide in the heavy and light version.
We are analyzing samples of recombinant protein which were incubated with small molecules that attach covalently to cysteine. The objective is to identify the positions of modification and extract the chromatograms of the labeled peptides for characterization. Essentially I define the molecule's formula in MaxQuant (saved in the modifications.xml file) and define both the molecule and carbamidomethyl as variable modifications. The analysis by MaxQuant clearly identifies peptides containing the molecule as well as their sequence and the exact labeling site (including if there are two cysteines in the same peptide). My objective was to import the peptide search into skyline to build a spectra library and to extract the chromatograms of the carbamidomethyl and molecule-bound peptides. However, the peptides with the bound molecule are never added to the library - only carbamidomethyl peptides are. This is even though MaxQuant clearly identifies the modified peptides and they are defined in the same way.
Is there anything you can recommend to help in this problem?
Details: Windows server R2 enterprise 64 bit
Skyline 64 bit 18.104.22.16805
I attach the screenshot from skyline. Cysteine containing peptides are added to the library (carbamidomethyl containing) and some are not (molecule-labeled).
I also attach the screen shot from the MaxQuant output showing the identification of the molecule-labeled peptide.
I am trying to figure out how to change the settings so that a charge state above +6 can be selected for a peptide's charge state for MS1 analysis. I noticed there was an older post about this from 2012 but the instructions on how find the setting to change was not clear and was for version 1.3. I suspect the interface has changed since then. Is there a tutorial out there that covers this?
Thanks in advance.
I would like to install Skyline 64bit on my computer but I have a problem to run the setup.exe file.
I have this message from Skyline Setup:
"An error occurred trying to download https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application"
Can you help me?
I have a very general question regarding error distribtion in quant proteomics experiments. Often the standard deviation and therefore the p-value is calculated using log values of the extracted ion chromatogramm areas. By using the log values instead of the original values you will get a completely different distribution and a much lower relative standard error! Why do people use the log areas instead of the original values? In my very small understanding of statistics, this artifically improves the test statistic and makes the results better than they appear! I would be very happy about an explanation because we have an in-house developed cross-link quant software which also does it in that way and I would really like to understand the background!
Thanks a lot in advance
Is it possible to get the daily update as a .msi file? We don't have internet access from the server we use Skyline on, so we need an offline installer.
Dear Skyline Team,
Thank you for your continued development of this excellent software package.
I am having trouble importing a timsTOF Pro file. The instrument was set up to collect scheduled PRM data for 34 isotope labeled peptides. When the results are imported into Compass DataAnalysis software, it appears that the method worked as anticipated - precursors are observed in the MS1 chromatogram and corresponding MS/MS are generated within the specified windows. However, when importing the results into Skyline Daily (22.214.171.124), no precursor and no product ions are found.
I've successfully imported other targeted runs from the timsTOF. Only this scheduled method is causing problems. Any insight you can provide would be appreciated. Thanks.
Hello! I just updated my skyline line for small molecules and I seeing this error. What does this mean? Thank you!
Failure opening S:\Departments\Analytics\BioAnalytics\Chia-Wei\QQQ-Demo\skyline_data analysis\troubleshooting skyline_falcon QQQ\032420_Troubleshooting_skyline_QQQ_falcon.sky.
The file contains an error on line 652 at column 9.
OK More Info
System.Reflection.TargetInvocationException: There is an error in XML document (652, 9). ---> System.InvalidOperationException: There is an error in XML document (652, 9). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 88.02 does not match calculated value 148.1
at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1973
at pwiz.Skyline.Util.Assume.IsTrue(Boolean condition, String error) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1932
at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1396
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1382
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1271
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1140
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1066
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 898
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 767
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 738
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 579
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 545
at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1960
at System.Xml.Serialization.XmlSerializationReader.ReadSerializable(IXmlSerializable serializable, Boolean wrappedAny)
--- End of inner exception stack trace ---
at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
at System.Xml.Serialization.XmlSerializer.Deserialize(TextReader textReader)
at pwiz.Skyline.SkylineWindow.<>c__DisplayClass979_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 322
at pwiz.Skyline.Util.ProgressWaitBroker.PerformWork(ILongWaitBroker broker) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\UtilUI.cs:line 125
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 246
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1909
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 194
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 131
at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 316