Generating spectral library from mzid output

[SimionKreimer]

Hi I'm attempting to use the output from PeptideShaker (after a SearchGUI data search) to generate a spectral library for Data Independent Acquisition (DIA) analysis. However I am unable to convert the mzid output into a usable format for SpectraST, which takes PeptideProphet pepXML as input. IDconvert in pPoteowizard produces an error when converting the PeptideShaker output and IDFileConverter, while able to convert the files, loses the spectrum reference information and the resulting pepXML file cannot be used to build a spectral library. Could you possibly provide a reliable parser for mzid that can emulate the peptideprophet pepxml output (and ProteinProphet if you really want to make my week)? Building a spectral library from DDA data and then using it for peptide-centric analysis of DIA data is a widely used workflow in the MS community. In my opinion, combining multiple search algorithms in PeptideShaker gives comprehensive results, better than Trans-Proteomic Pipeline and Proteome Discoverer, but it's very disappointing that the output is incompatible with other important data analysis tools, which were developed to accept the PeptideProphet output. Best, Simion

[mvaudel]

Hi Simion,

Would it be an option for you to use Skyline? If you try the current daily build it loads PeptideShaker mzIdentML files :-)

We have TPP compatible exports on the todo list but I am not sure when we will be able to release this feature. Do you know anyone who would be willing to contribute on this?

I understand that it is very frustrating to get stuck in the middle of a pipeline for a format issue. But as we already discussed in a previous thread, we are not the limiting factor here, as we comply with the current standards of the field. Did you notify your problem to the developers of SpectraST? Also, did you not find a solution with OpenMS?

Best regards,

Marc

[hbarsnes]

Hi Simion,

I just tested the latest version of idconvert from ProteoWizard v3.0.9013 and I was able to create pepXML without any errors using the command line below:

C:\Program Files\ProteoWizard\ProteoWizard 3.0.9013>idconvert "path-to-mzid.file"/psMzidFile.mzid --pepXML -v -o C:\Users\hba041\temp\pepxml

Is this not working on your side? Please make sure that the mzid file was created using the latest version of PeptideShaker.

Best regards, Harald

[SimionKreimer]

Hi Marc and Harald, I've tried idconvert with PS 1.1.2 output and proteowiz3.0.9016, and the conversion finished with no errors, but the pepXML is rather useless. It only includes results from 1 file of the 8 in the in the original mzidentML and doesn't seem to have the PS scores, just scores from individual engines. As I mentioned, the OpenMS (IDFileConverter) solution works for some applications, but in this case the spectrum information was removed from the pepXML so it is not suitable for building a spectral library. As I'm sure you are aware, it's not easy getting developers to adjust their input and output formats. So I've reached a bit of a dead end in that direction as well. Unfortunately my group is not very strong in the programming department so we cannot contribute. I need to make a traML iRT calibrated spectral library, using an OpenSWATH + SpectraST pipeline, and switching between spectral library formats is even more difficult than identification files, so Skyline will not help there. Although it's good news that they're now able to import mzidentML. Just thought I'd ask again, as I do really like the software, but can't use it in my workflows due to these compatibility issues. Best, Simion

[mvaudel]

Hi Simion,

Thanks for all these details it is very instructive. It seems that you are uncovering why we don't support pepXML: depending on the tool every pepXML file is different, so we basically not only need to write pepXML but write the specific flavour expected by a given pipeline. This is typically poorly documented if documented at all, so supporting and maintaining these exports is a very time consuming task. Finally, pepXML does not allow us to put the information we have in PeptideShaker, so in the end you might even end up not being able to use this file at all. I am not sure to which extend we can fix it but I can try to look into it if I get some time.

On a more positive note, I have been in contact with OpenSWATH people to make our tools compatible, so we might be able to bypass the problem. We are also working on the combination with DIA Umpire, so with the support of Skyline that gives you a nice panel of DIA pipelines :) Is there any specific reason why you need to use OpenSWATH + SpectraST?

Best regards,

Marc

2015-10-21 0:42 GMT+02:00 SimionKreimer notifications@github.com:

Hi Marc and Harald, I've tried idconvert with PS 1.1.2 output and proteowiz3.0.9016, and the conversion finished with no errors, but the pepXML is rather useless. It only includes results from 1 file of the 8 in the in the original mzidentML and doesn't seem to have the PS scores, just scores from individual engines. As I mentioned, the OpenMS (IDFileConverter) solution works for some applications, but in this case the spectrum information was removed from the pepXML so it is not suitable for building a spectral library. As I'm sure you are aware, it's not easy getting developers to adjust their input and output formats. So I've reached a bit of a dead end in that direction as well. Unfortunately my group is not very strong in the programming department so we cannot contribute. I need to make a traML iRT calibrated spectral library, using an OpenSWATH + SpectraST pipeline, and switching between spectral library formats is even more difficult than identification files, so Skyline will not help th ere. Alt hough it's good news that they're now able to import mzidentML. Just thought I'd ask again, as I do really like the software, but can't use it in my workflows due to these compatibility issues. Best, Simion

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-149723320 .

[SimionKreimer]

To make an external library for DIA Umpire :)

[SimionKreimer]

Actually both threads were about trying to the get DIA Umpire to work with SearchGUI, and I'm glad that you're working on integrating that very important tool with your software. When you have some beta version ready I would be glad to test it.

[1Moe]

Hi, new to the DIA field and getting my head around it slowly. I also tried to build a skyline library from a peptideshaker mzid file.

My workflow (for a quick test): Human plasma (no fractionation/or immunoprecipitation), 4 injections, 2h gradient, DDA on an AbSciex TripleTof 5600 Conversion of wiff files to mgf files with ABSciex mgf converter Load mgf files into SearchGui and search with 3 engines (X!tandem, MSAmanda, and Comet) Automatic analysis in PeptideShaker, saved as cpsx file Export to mzid file using PeptideShaker

Generation of Libraries: In latest skyline-daily (64-bit) 3.1.1.9007, go to build library, choose the mzid file and ensure that the original mgf files are in the same folder as the mzid file I also set a background proteome in skyline (latest reviewed human proteome from uniprot+reversedecoy) Then explored the generated library in skyline and associated all peptides with proteins of the background proteome

Outcome: Skyline tells me that it imported 214 proteins/ 1112 peptides/ 1353 precursors and 4052 transitions (3 most intense per precursor)

Questions: 1) Which peptides from the entire PeptideShaker project are included in the mzid file? What are the filter settings to qualify a peptide to go through to the mzid file and can I change this filter prior or post export of the mzid file itself?

2) what info does skyline get out of the original mgf files during library generation? shouldn't all the info be in the mzid file?

3) How do I best combine the search output from PD1.4 mascot search (msf reports) with mzid reports?

[mvaudel]

Hi and thank you for your message,

1) In the present form we export all ids without filtering - even the decoys. This is because the support is very new and we did not have the time to fine tune the settings. A new version will come very soon with more possibilities of filtering - hopefully when the official Skyline release is out :)

2) The mzid file contains only identification results, Skyline needs the original spectra, hence the need for mgf, mzML, or mzXML files. For this, keep your spectrum file(s) next to the mzid file and Skyline will handle it automatically. Again, this will be automatically done by PeptideShaker in a very near future.

3) I am not aware of such a possibility, but you can integrate the Mascot results with your other search engines in PeptideShaker. For this, select the Mascot .dat files when setting up your PeptideShaker project. Make sure that you have run the searches with the same search parameters, mgf, and fasta files, and that the decoy option in Mascot is disabled. You might also want to try some of the other free search engines from SearchGUI, they give very nice results :) You can monitor the performance of the search engines in the SpectrumID tab of PeptideShaker, their relative performance tends to vary from one search to the other.

Hope that helps!

Best regards,

Marc

2015-10-23 2:50 GMT+02:00 1Moe notifications@github.com:

Hi, new to the DIA field and getting my head around it slowly. I also tried to build a skyline library from a peptideshaker mzid file.

My workflow (for a quick test): Human plasma (no fractionation/or immunoprecipitation), 4 injections, 2h gradient, DDA on an AbSciex TripleTof 5600 Conversion of wiff files to mgf files with ABSciex mgf converter Load mgf files into SearchGui and search with 3 engines (X!tandem, MSAmanda, and Comet) Automatic analysis in PeptideShaker, saved as cpsx file Export to mzid file using PeptideShaker

Generation of Libraries: In latest skyline-daily (64-bit) 3.1.1.9007, go to build library, choose the mzid file and ensure that the original mgf files are in the same folder as the mzid file I also set a background proteome in skyline (latest reviewed human proteome from uniprot+reversedecoy) Then explored the generated library in skyline and associated all peptides with proteins of the background proteome

Outcome: Skyline tells me that it imported 214 proteins/ 1112 peptides/ 1353 precursors and 4052 transitions (3 most intense per precursor)

Questions: 1) Which peptides from the entire PeptideShaker project are included in the mzid file? What are the filter settings to qualify a peptide to go through to the mzid file and can I change this filter prior or post export of the mzid file itself?

2) what info does skyline get out of the original mgf files during library generation? shouldn't all the info be in the mzid file?

3) How do I best combine the search output from PD1.4 mascot search (msf reports) with mzid reports?

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-150396998 .

[1Moe]

Thanks Marc,

this helped a lot. 1) It certainly will be a great improvement when the filtering is working. Rather than using all validated PSMs I would use filtering to build custom libraries (e.g. confidence >99, score>99, validatedpeptides>1, validatedPSMs>5. 2,3) Thanks for the info! The info on the SpectrumID tab is great. Is it possible for you to improve the export options to get high resolution images?

[mvaudel]

Hi again,

Great to hear that you find this useful!

1) yes, will take care of this. In the meantime note that you can already use confidence>99% to validate your matches. Also, if you want to select the proteins with validatedpeptides>1, validatedPSMs>5, you can set these as additional QC filters, then they will appear in green and the validated proteins not passing the filters will be in yellow. By default this is set to 2 confident peptides and 2 confident PSMs but this can be changed via the "Edit" -> "Validation Filters" menu.

2,3) If you export the illustrations as svg using the triangle to the top right of every display it should be high resolution :)

Best regards,

Marc

[hbarsnes]

Hi,

Just a quick comment on the export of the Spectrum IDs tab plots.

It turns out that our high resolution exports is not currently working that way it should for these specific plots. I will look into it and make sure that it is fixed in the next release.

Thanks for making us aware of this issue.

Best regards, Harald

[mvaudel]

Hi again Simion,

Would you have an example file for me to see how much work it would be to support this?

Best regards,

Marc

2015-10-20 20:09 GMT+02:00 SimionKreimer notifications@github.com:

Hi I'm attempting to use the output from PeptideShaker (after a SearchGUI data search) to generate a spectral library for Data Independent Acquisition (DIA) analysis. However I am unable to convert the mzid output into a usable format for SpectraST, which takes PeptideProphet pepXML as input. IDconvert in pPoteowizard produces an error when converting the PeptideShaker output and IDFileConverter, while able to convert the files, loses the spectrum reference information and the resulting pepXML file cannot be used to build a spectral library. Could you possibly provide a reliable parser for mzid that can emulate the peptideprophet pepxml output (and ProteinProphet if you really want to make my week)? Building a spectral library from DDA data and then using it for peptide-centric analysis of DIA data is a widely used workflow in the MS community. In my opinion, combining multiple search algorithms in PeptideShaker gives comprehensive results, better than Trans-Proteomic Pipeline and Proteome Discoverer, but it's very disappointing that the output is incompatible with other important data analysis tools, which were developed to accept the PeptideProphet output. Best, Simion

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94.

[SimionKreimer]

Hi Marc, Thank you for considering this enhancement. Spectra ST accepts result files in the Peptide Prophet pepXML format and requires that the spectrum numbers and source file names remain intact (this is where the Open MS IDFileConverter fails, and they don't support this feature anymore). The DIA Umpire quantification module requires a separate file that contains the cumulative probability score for each protein in addition to the peptide result files (also in peptide prophet pepXML). I've placed examples of the pepXML and prot.XML files into this Dropbox folder: https://www.dropbox.com/sh/mviulbjhvw9fks6/AADl-PXQ_CaT1Fql7TDqubSya?dl=0

[1Moe]

Hi Marc, I'm loving PeptideShaker and SearchGui, thanks for all the efforts you and your team are putting into it.

Some comments/questions 1) The new skyline version 3.5 is out now and I was wondering whether the "export to skyline" option will include filtering options in any near future updates. Or, perhaps you know of a workflow that allows me to build a spectral library in skyline using other PeptideShaker export features (validated proteins with validated peptides with validated PSMs). Alternatively, is there an option to hide or delete all proteins that do not meet my validation criteria (e.g. FDR of 1%, >2 peptides, >5 spectra), then I could export only those left over using the export to Skyline function.

2) I also was wondering for future versions if you could include filtering or sorting of multiple columns (e.g. sort with user-defined column priorities, so that I could sort by "Validated", then by "#Peptides", "#Spectra", and "Protein Inference")

3) It would be great if the QC plots could also be displayed per fraction (not "just" overall). An easy export functionality for QC plots would also be great to do some statistics outside of Peptideshaker. I would use this QC of fractions to decide on sample quality and to assess sample prep. methods, e.g. by plotting individual fractions and assessing: Peptide charge distribution Number or percentage of total/identified/validated peptides Number of missed cleavages

4) Probably out of scope of peptide shaker, but having a visualisation of the raw data (before database search) with a few analysis tools would be helpful for QC as well. e.g. the chromatographic TIC, to check reproducibility and peptide area variability (CV)

Thanks again for the great work! best wishes Moe

[mvaudel]

Hi Moe,

Thanks for the kind feedback, it is really appreciated. Here are answers for the specific points:

1) We are working on implementing some filters. We are currently gathering ideas on this and will implement the most popular suggestions, see the following thread: https://groups.google.com/forum/#!topic/peptide-shaker/4nuDGQM4vt4

2) You can apply filters via the "Edit" -> "Filters" menu, and either hide or highlight hits accordingly. Would that answer your need?

3) We have been wanting to do this since quite some time, but never had the opportunity to get to this I am afraid, we are only two and have a lot of things on the list already :) If you or anyone would like to contribute on this I can guide you through the code.

4) You are correct, this is quite out of the scope. For these tasks we rely on commercial software. Among academic software, maybe SIMPATIQCO ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558011/) could do it? Once again, we would be very happy to provide a solution of our own but we don't have the workforce... We are open to collaborations though :)

Best regards,

Marc

2015-12-15 5:10 GMT+01:00 1Moe notifications@github.com:

Hi Marc, I'm loving PeptideShaker and SearchGui, thanks for all the efforts you and your team are putting into it.

Some comments/questions 1) The new skyline version 3.5 is out now and I was wondering whether the "export to skyline" option will include filtering options in any near future updates. Or, perhaps you know of a workflow that allows me to build a spectral library in skyline using other PeptideShaker export features (validated proteins with validated peptides with validated PSMs). Alternatively, is there an option to hide or delete all proteins that do not meet my validation criteria (e.g. FDR of 1%, >2 peptides, >5 spectra), then I could export only those left over using the export to Skyline function.

2) I also was wondering for future versions if you could include filtering or sorting of multiple columns (e.g. sort with user-defined column priorities, so that I could sort by "Validated", then by "#Peptides", "#Spectra", and "Protein Inference")

3) It would be great if the QC plots could also be displayed per fraction (not "just" overall). An easy export functionality for QC plots would also be great to do some statistics outside of Peptideshaker. I would use this QC of fractions to decide on sample quality and to assess sample prep. methods, e.g. by plotting individual fractions and assessing: Peptide charge distribution Number or percentage of total/identified/validated peptides Number of missed cleavages

4) Probably out of scope of peptide shaker, but having a visualisation of the raw data (before database search) with a few analysis tools would be helpful for QC as well. e.g. the chromatographic TIC, to check reproducibility and peptide area variability (CV)

Thanks again for the great work! best wishes Moe

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-164639644 .

[1Moe]

Hi Marc,

1) I will post some of my suggestions here. https://groups.google.com/forum/#!topic/peptide-shaker/4nuDGQM4vt4

2) I am struggling with the applications of filters via the "Edit" -> "Filters" menu. When I go to Add Filter I can't see or activate anything in the "Filter Items" form. Right/left clicking doesn't open any sub-menu and there is no drop-down menu where I can select filter items from. I also encounter this when I try to add a filter in "Edit" -> "Validation Filters" menu. I know how to change existing filters there but I can't add new filters. It would be great if you could let me know how to do this.

3) I'd love to help but unfortunately I don't have any coding experience - something I should improve on!

4) Thanks for the link to SIMPATIQCO ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558011/) I'll look into it but might have to convert my wiff files. Which commercial software do you use?

Best regards,

Moe

On 15 December 2015 at 20:36, Marc Vaudel notifications@github.com wrote:

Hi Moe,

Thanks for the kind feedback, it is really appreciated. Here are answers for the specific points:

1) We are working on implementing some filters. We are currently gathering ideas on this and will implement the most popular suggestions, see the following thread: https://groups.google.com/forum/#!topic/peptide-shaker/4nuDGQM4vt4

2) You can apply filters via the "Edit" -> "Filters" menu, and either hide or highlight hits accordingly. Would that answer your need?

3) We have been wanting to do this since quite some time, but never had the opportunity to get to this I am afraid, we are only two and have a lot of things on the list already :) If you or anyone would like to contribute on this I can guide you through the code.

4) You are correct, this is quite out of the scope. For these tasks we rely on commercial software. Among academic software, maybe SIMPATIQCO ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558011/) could do it? Once again, we would be very happy to provide a solution of our own but we don't have the workforce... We are open to collaborations though :)

Best regards,

Marc

2015-12-15 5:10 GMT+01:00 1Moe notifications@github.com:

Hi Marc, I'm loving PeptideShaker and SearchGui, thanks for all the efforts you and your team are putting into it.

Some comments/questions 1) The new skyline version 3.5 is out now and I was wondering whether the "export to skyline" option will include filtering options in any near future updates. Or, perhaps you know of a workflow that allows me to build a spectral library in skyline using other PeptideShaker export features (validated proteins with validated peptides with validated PSMs). Alternatively, is there an option to hide or delete all proteins that do not meet my validation criteria (e.g. FDR of 1%, >2 peptides, >5 spectra), then I could export only those left over using the export to Skyline function.

2) I also was wondering for future versions if you could include filtering or sorting of multiple columns (e.g. sort with user-defined column priorities, so that I could sort by "Validated", then by "#Peptides", "#Spectra", and "Protein Inference")

3) It would be great if the QC plots could also be displayed per fraction (not "just" overall). An easy export functionality for QC plots would also be great to do some statistics outside of Peptideshaker. I would use this QC of fractions to decide on sample quality and to assess sample prep. methods, e.g. by plotting individual fractions and assessing: Peptide charge distribution Number or percentage of total/identified/validated peptides Number of missed cleavages

4) Probably out of scope of peptide shaker, but having a visualisation of the raw data (before database search) with a few analysis tools would be helpful for QC as well. e.g. the chromatographic TIC, to check reproducibility and peptide area variability (CV)

Thanks again for the great work! best wishes Moe

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-164639644

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-164673779 .

[hbarsnes]

Hi Moe,

Regarding the issues with the filters, this was due to a bug in our code where only mouse clicks on the table rows where registered (and not for the table background). Hence it was impossible to get the popup menu (with the Add/Remove) when there where no rows in the table. This has now been fixed and a new version will be released as soon as possible.

Best regards, Harald

[1Moe]

Hi Harald, thanks a lot for your quick reply, much appreciated. Looking forward to the new version :) I may have another bug to report to you and Marc to do with mzXML files as input for SearchGui. It is not stopping me from using SearchGui but maybe interesting for other people.

I usually use qtofpeakpicker to convert my wiff files to mzXML files with the following command (according to the Schubert paper 2015).

"C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\qtofpeakpicker.exe" -I test.wiff -O test.mzXML --resolution=20000 --area=1 --threshold=1 --smoothwidth=1.1

When I try to load the generated mzXML files into SearchGUI I get an error message saying that there is no mgf file. My guess is that there may be a problem with MSConvert.

However, I can easily convert the mzXML file to an .mgf file myself with MSConvert using either the MSConvertGUI or the following command: "C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\msconvert.exe" test.mzXML --mgf --filter "threshold count 150 most-intense" --outfile test150.mgf

I can subsequently easily use the generated mgf file in SearchGui. Cheers Moe

On 18 December 2015 at 11:07, Harald Barsnes notifications@github.com wrote:

Hi Moe,

Regarding the issues with the filters, this was due to a bug in our code where only mouse clicks on the table rows where registered (and not for the table background). Hence it was impossible to get the popup menu (with the Add/Remove) when there where no rows in the table. This has now been fixed and a new version will be released as soon as possible.

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165594192 .

[ulrich-eckhard]

Hey Moe,

think PeptideShaker just doesn't support mzXML yet. see: http://compomics.github.io/projects/peptide-shaker.html#converting-spectrum-data

---

Converting Spectrum Data PeptideShaker currently only supports mgf files as the input format for the spectra. To convert your raw data to mgf we recommend using msconvert from ProteoWizard.

[1Moe]

Thanks Ulrich!

On 18 December 2015 at 15:26, Ulrich Eckhard notifications@github.com wrote:

Hey Moe,

think PeptideShaker just doesn't support mzXML yet. see:

http://compomics.github.io/projects/peptide-shaker.html#converting-spectrum-data

Converting Spectrum Data PeptideShaker currently only supports mgf files as the input format for the spectra. To convert your raw data to mgf we recommend using msconvert from ProteoWizard.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165649277 .

[ulrich-eckhard]

I am happy that I could finally help someone. Typically I need all the help from Marc and Harald! :-)

[mvaudel]

Hi Moe, hi Ulrich,

Sorry our msconvert options are tuned for Orbitrap instrument, we have very little experience with QTOF.

When selecting your mzXML files in SearchGUI, msconvert should convert them, but my guess is that it does not manage to apply the peak picker on the already peak picked files. Do you have more information on when the error occurs? Does msconvert start at all?

If yes, can you try to click on the cogwheel next to msconvert, remove the peak picker, and add your filter "threshold count 150 most-intense"?

On the long term, we could run the qtof peak picker on wiff files, if it is something generic for wiff files. Then you can directly select your wiff files in SearchGUI. Would that be an option?

Best regards,

Marc

2015-12-18 3:12 GMT+01:00 1Moe notifications@github.com:

Hi Harald, thanks a lot for your quick reply, much appreciated. Looking forward to the new version :) I may have another bug to report to you and Marc to do with mzXML files as input for SearchGui. It is not stopping me from using SearchGui but maybe interesting for other people.

I usually use qtofpeakpicker to convert my wiff files to mzXML files with the following command (according to the Schubert paper 2015).

"C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\qtofpeakpicker.exe" -I test.wiff -O test.mzXML --resolution=20000 --area=1 --threshold=1 --smoothwidth=1.1

When I try to load the generated mzXML files into SearchGUI I get an error message saying that there is no mgf file. My guess is that there may be a problem with MSConvert.

However, I can easily convert the mzXML file to an .mgf file myself with MSConvert using either the MSConvertGUI or the following command: "C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\msconvert.exe" test.mzXML --mgf --filter "threshold count 150 most-intense" --outfile test150.mgf

I can subsequently easily use the generated mgf file in SearchGui. Cheers Moe

On 18 December 2015 at 11:07, Harald Barsnes notifications@github.com wrote:

Hi Moe,

Regarding the issues with the filters, this was due to a bug in our code where only mouse clicks on the table rows where registered (and not for the table background). Hence it was impossible to get the popup menu (with the Add/Remove) when there where no rows in the table. This has now been fixed and a new version will be released as soon as possible.

Best regards, Harald

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165594192

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165646054 .

[hbarsnes]

Hi Moe, hi Ulrich,

@Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

[ulrich-eckhard]

hmmm ... was not aware of that option but good to know. but somehow - as a gut feeling, I think it is better if people provide a mgf right away. too much can go wrong during file conversion (or not necessarily wrong, but you can get very different results depending on your msConvert settings - especially for QTof data), thus I am not sure if you really want that hassle covered within SearchGUI.

On Fri, Dec 18, 2015 at 7:32 AM, Harald Barsnes notifications@github.com wrote:

Hi Moe, hi Ulrich,

@Ulrich https://github.com/Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165806805 .

[mvaudel]

Hi all,

I guess you don't have an infinite set of parameters for msconvert, maybe we can make a default configurations for your instrument?

Back in the days when I was working on such instruments I was doing the signal processing using OpenMS. They have very nice algorithms, you could easily reuse workflows and inspect the results, maybe that is an alternative to generate the mgf?

Best regards,

Marc

2015-12-18 16:52 GMT+01:00 Ulrich Eckhard notifications@github.com:

hmmm ... was not aware of that option but good to know. but somehow - as a gut feeling, I think it is better if people provide a mgf right away. too much can go wrong during file conversion (or not necessarily wrong, but you can get very different results depending on your msConvert settings - especially for QTof data), thus I am not sure if you really want that hassle covered within SearchGUI.

On Fri, Dec 18, 2015 at 7:32 AM, Harald Barsnes notifications@github.com wrote:

Hi Moe, hi Ulrich,

@Ulrich https://github.com/Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165806805

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165812838 .

[ulrich-eckhard]

definitely true. usually try to stick with the vendor software (if possible). gave me nearly always best results (even though msConvert is great and i used it a lot for orbi data), especially for QTof data. but that's a personal experience of course. it also can take quite a while. e.g raw data from a bruker impact II are typically around 8GB. just think it is better to do the conversions outside of SearchGui (with whatever program people prefer). but definitely just a personal opinion. On Dec 18, 2015 8:21 AM, "Marc Vaudel" notifications@github.com wrote:

Hi all,

I guess you don't have an infinite set of parameters for msconvert, maybe we can make a default configurations for your instrument?

Back in the days when I was working on such instruments I was doing the signal processing using OpenMS. They have very nice algorithms, you could easily reuse workflows and inspect the results, maybe that is an alternative to generate the mgf?

Best regards,

Marc

2015-12-18 16:52 GMT+01:00 Ulrich Eckhard notifications@github.com:

hmmm ... was not aware of that option but good to know. but somehow - as a gut feeling, I think it is better if people provide a mgf right away. too much can go wrong during file conversion (or not necessarily wrong, but you can get very different results depending on your msConvert settings - especially for QTof data), thus I am not sure if you really want that hassle covered within SearchGUI.

On Fri, Dec 18, 2015 at 7:32 AM, Harald Barsnes < notifications@github.com> wrote:

Hi Moe, hi Ulrich,

@Ulrich https://github.com/Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165806805

.

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165812838

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165823799 .

[1Moe]

Hi all, Regarding conversion, the Supplementary info in Schubert et al 2015 suggests that qtofpeakpicker does a better job than AbSciex converter for peakpicking of Sciex QTof data. It would be nice if I could upload wiff files directly into SearchGui!!!

At this stage I haven't tested extensively but removing the peak picking filter in SearchGui's MSConvert doesn't seem to work. I still get the same error: Mon Dec 21 11:07:27 NZDT 2015 Processing test.mzXML with msconvert.

Mon Dec 21 11:07:27 NZDT 2015 msconvert finished for test.mzXML (295 milliseconds).

Mon Dec 21 11:07:27 NZDT 2015 Indexing spectrum files. Mon Dec 21 11:07:27 NZDT 2015 Error: C:\test.mgf (The system cannot find the file specified) Mon Dec 21 11:07:27 NZDT 2015 An error occurred while running SearchGUI. Please contact the developers. Mon Dec 21 11:07:27 NZDT 2015 The search or processing did not finish properly!

Mon Dec 21 11:07:27 NZDT 2015 Search Canceled!

Cheers Moe

On 19 December 2015 at 07:07, Ulrich Eckhard notifications@github.com wrote:

definitely true. usually try to stick with the vendor software (if possible). gave me nearly always best results (even though msConvert is great and i used it a lot for orbi data), especially for QTof data. but that's a personal experience of course. it also can take quite a while. e.g raw data from a bruker impact II are typically around 8GB. just think it is better to do the conversions outside of SearchGui (with whatever program people prefer). but definitely just a personal opinion.

On Dec 18, 2015 8:21 AM, "Marc Vaudel" notifications@github.com wrote:

Hi all,

I guess you don't have an infinite set of parameters for msconvert, maybe we can make a default configurations for your instrument?

Back in the days when I was working on such instruments I was doing the signal processing using OpenMS. They have very nice algorithms, you could easily reuse workflows and inspect the results, maybe that is an alternative to generate the mgf?

Best regards,

Marc

2015-12-18 16:52 GMT+01:00 Ulrich Eckhard notifications@github.com:

hmmm ... was not aware of that option but good to know. but somehow - as a gut feeling, I think it is better if people provide a mgf right away. too much can go wrong during file conversion (or not necessarily wrong, but you can get very different results depending on your msConvert settings - especially for QTof data), thus I am not sure if you really want that hassle covered within SearchGUI.

On Fri, Dec 18, 2015 at 7:32 AM, Harald Barsnes < notifications@github.com> wrote:

Hi Moe, hi Ulrich,

@Ulrich https://github.com/Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165806805

.

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165812838

.

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165823799

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165859010 .

[mvaudel]

Hi Moe,

It is rather surprising that msconvert finishes in less than 0.3 seconds, looks like something is going wrong there. Would it be possible for you to send me the mzXML file?

Best regards,

Marc

2015-12-20 23:14 GMT+01:00 1Moe notifications@github.com:

Hi all, Regarding conversion, the Supplementary info in Schubert et al 2015 suggests that qtofpeakpicker does a better job than AbSciex converter for peakpicking of Sciex QTof data. It would be nice if I could upload wiff files directly into SearchGui!!!

At this stage I haven't tested extensively but removing the peak picking filter in SearchGui's MSConvert doesn't seem to work. I still get the same error: Mon Dec 21 11:07:27 NZDT 2015 Processing test.mzXML with msconvert.

Mon Dec 21 11:07:27 NZDT 2015 msconvert finished for test.mzXML (295 milliseconds).

Mon Dec 21 11:07:27 NZDT 2015 Indexing spectrum files. Mon Dec 21 11:07:27 NZDT 2015 Error: C:\test.mgf (The system cannot find the file specified) Mon Dec 21 11:07:27 NZDT 2015 An error occurred while running SearchGUI. Please contact the developers. Mon Dec 21 11:07:27 NZDT 2015 The search or processing did not finish properly!

Mon Dec 21 11:07:27 NZDT 2015 Search Canceled!

Cheers Moe

On 19 December 2015 at 07:07, Ulrich Eckhard notifications@github.com wrote:

definitely true. usually try to stick with the vendor software (if possible). gave me nearly always best results (even though msConvert is great and i used it a lot for orbi data), especially for QTof data. but that's a personal experience of course. it also can take quite a while. e.g raw data from a bruker impact II are typically around 8GB. just think it is better to do the conversions outside of SearchGui (with whatever program people prefer). but definitely just a personal opinion.

On Dec 18, 2015 8:21 AM, "Marc Vaudel" notifications@github.com wrote:

Hi all,

I guess you don't have an infinite set of parameters for msconvert, maybe we can make a default configurations for your instrument?

Back in the days when I was working on such instruments I was doing the signal processing using OpenMS. They have very nice algorithms, you could easily reuse workflows and inspect the results, maybe that is an alternative to generate the mgf?

Best regards,

Marc

2015-12-18 16:52 GMT+01:00 Ulrich Eckhard notifications@github.com:

hmmm ... was not aware of that option but good to know. but somehow - as a gut feeling, I think it is better if people provide a mgf right away. too much can go wrong during file conversion (or not necessarily wrong, but you can get very different results depending on your msConvert settings - especially for QTof data), thus I am not sure if you really want that hassle covered within SearchGUI.

On Fri, Dec 18, 2015 at 7:32 AM, Harald Barsnes < notifications@github.com> wrote:

Hi Moe, hi Ulrich,

@Ulrich https://github.com/Ulrich: you are only partly correct. ;)

It is correct that SearchGUI itself only supports mgf as input, but if raw files are provided (including mzML and mzXML) and ProteoWizard is installed, SearchGUI will attempt to convert the files to mgf using msconvert.

As Marc already mentioned, we have little experience with converting wiff files, but I see no reason why it should not be possible to convert your generated mzXML file to mgf.

The general msconvert command line we used is: msconvert "path\qExactive01819.raw" -o "path\data" --mgf -v --filter "peakPicking "

Pretty sure I tested this for mzXML files as well (but from .raw files not .wiff). Would be nice to know what sort of error message you get from mscovert?

Note that you can edit the filters used by msconvert by clicking the cogwheel after the msconvert line in SearchGUI. However, most of the filters are untested from our side. But it could be as easy as removing the peak picking filter (and adding your own intensity filter)?

Best regards, Harald

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165806805

.

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165812838

.

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165823799

.

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-165859010

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-166158700 .

[1Moe]

Hi Marc, how do I send you big files (10-1000MB)? cheers Moe

[mvaudel]

Hi Moe,

Is it an option to put them in DropBox, Google Drive or similar big file attachment solution?

Best regards,

Marc

2015-12-23 2:39 GMT+01:00 1Moe notifications@github.com:

Hi Marc, how do I send you big files (10-1000MB)? cheers Moe

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-166774446 .

[1Moe]

Hi all

first of all, happy new year thanks a lot to Marc and Harald for bringing back the Validation Filter functionality in the new version of PeptideShaker!!!

Regarding problems with conversion of mzXML file to mgf file: I've uploaded the mzXML file generated from the corresponding wiff and wiff.scan files with qtofpeakpicker

https://drive.google.com/folderview?id=0BybCLLWRgDsUX2VTc0F1ZlpCMnM&usp=sharing.

I used the following qtofpeakpicker command "C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\qtofpeakpicker.exe" -I test.wiff -O test.mzXML --resolution=20000 --area=1 --threshold=1 --smoothwidth=1.1

searchgui is not able to convert this mzXML file to mgf, however, when I use msconvert from the command line

I then proceed to convert to mgf with msconvert "C:\Program Files\ProteoWizard\ProteoWizard 3.0.8934\msconvert.exe" test.mzXML --mgf --filter "threshold count 150 most-intense" --outfile test150.mgf

searchgui can accept the mgf file just fine! cheers Moe

[1Moe]

Hi Marc,

what is the best way to build a spectral library from a peptideshaker output? I just tried the library build function in the new skyline version (3.5) with a mzid export from peptideshaker. Previously this worked for me (see comment further above). Now skyline reports an error (not sure if this is a skyline or a peptideshaker issue).

Below is the skyline error message, any ideas for a fix or better solution of how I can export validated proteins in a way that allows import into skyline? cheers Moritz

System.IO.IOException: ERROR: bad lexical cast: source type value could not be interpreted as target ERROR: ERROR: reading file peptideshakernew.mzid

at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status, TextWriter writer) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, ProgressStatus& status, String[]& ambiguous) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 166 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 119

[mvaudel]

Hi Moritz,

We did not have time to work on our Skyline export so there is nothing new there since last time, I will check later today if it still works on our side.

From the error message it looks like a formatting exception. Would it be possible for you to make the file available to us?

Best regards and sorry for the inconvenience,

Marc

2016-01-07 6:33 GMT+01:00 1Moe notifications@github.com:

Hi Marc,

what is the best way to build a spectral library from a peptideshaker output? I just tried the library build function in the new skyline version (3.5) with a mzid export from peptideshaker. Previously this worked for me (see comment further above). Now skyline reports an error (not sure if this is a skyline or a peptideshaker issue).

Below is the skyline error message, any ideas for a fix or better solution of how I can export validated proteins in a way that allows import into skyline? cheers Moritz

System.IO.IOException: ERROR: bad lexical cast: source type value could not be interpreted as target ERROR: ERROR: reading file peptideshakernew.mzid

at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status, TextWriter writer) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, ProgressStatus& status, String[]& ambiguous) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 166 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 119

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-169557444 .

[hbarsnes]

Below is the skyline error message, any ideas for a fix or better solution of how I can export validated proteins in a way that allows import into skyline?

I get the same error on the PeptideShaker example dataset when doing a new mzIdentML export. I will look into it and hopefully come up with a fix.

Best regards, Harald

[hbarsnes]

Hi again,

The mzIdentML (and PRIDE XML) export issue has now been fixed. The problem was in the new way we tried to escape non-standard characters. Please try PeptideShaker v1.3.5. It should allow you to load your data in Skyline again.

Best regards, Harald

[hbarsnes]

searchgui is not able to convert this mzXML file to mgf

I have no problems converting your mzXML file. Perhaps you can try updating ProteoWizard? As the one you are using (3.0.8934) is a bit old. Works for me with ProteoWizard 3.0.9134.

You need to play with the msconvert filters to get the same file as the one you have though. Just click the cogwheel after the msconvert line in SearchGUI, remove the peakpicking filter and add the threshold filter with "count 150 most-intense" as the value. Then resulting mgf should then be identical to your test150.mgf file. At least that is the case on my side.

Best regards, Harald

[1Moe]

Hi Harald,

thanks for the quick reply, the mzid import in skyline works now with the example data set from peptideshaker but not with my mzid file I generated. I've uploaded the mzid150 file to the folder https://drive.google.com/folderview?id=0BybCLLWRgDsUX2VTc0F1ZlpCMnM&usp=sharing. cheers moe

[hbarsnes]

Hi Moe,

I can load your mzid file without any problems in the latest version of Skyline. What sort of errors are you getting? Please make sure that you are using the latest version of Skyline.

BTW, in the next SearchGUI release you'll be able to convert the wiff files directly (via msconvert) as long as the wiff.scan files are located in the same folder as the related wiff files. The mgf files will not be identical though as the peak picking algorithms seem to be different. But maybe you can play around with the msconvert filter options to make them more similar. In the end I'm not sure how much it will affect the search results. But that is something to test as well I guess.

Best regards, Harald

[1Moe]

Hi Harald, I've got the latest version of skyline daily (64 bit, version 3.5.1.9226) and pwiz (64 bit) 3.0.9248-x86_64.

I get the following error when building a library in skyline

System.IO.IOException: ERROR: failed opening file: The system cannot find the file specified. ERROR: : iostream stream error ERROR: ERROR: reading file test150.mzid

at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status, TextWriter writer) in c:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, ProgressStatus& status, String[]& ambiguous) in c:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 166 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 119

On 8 January 2016 at 11:18, Harald Barsnes notifications@github.com wrote:

Hi Moe,

I can load your mzid file without any problems in the latest version of Skyline. What sort of errors are you getting? Please make sure that you are using the latest version of Skyline.

BTW, in the next SearchGUI release you'll be able to convert the wiff files directly (via msconvert) as long as the wiff.scan files are located in the same folder as the related wiff files. The mgf files will not be identical though as the peak picking algorithms seem to be different. But maybe you can play around with the msconvert filter options to make them more similar. In the end I'm not sure how much it will affect the search results. But that is something to test as well I guess.

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-169824298 .

[1Moe]

I'm starting to think something is not quite right with my pwiz. I've successfully converted a traml to tsv using TOPPAS. When I try to import this transition list csv file into skyline via import - transition lists I receive an error message.

Failed reading the file ...test.tsv. Unrecognized Unimod id 35 in modified peptide sequence

Below is more info. Would appreciate any help on this. regards, Moe

System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. ---> System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 277 at pwiz.Skyline.Model.ModificationMatcher.IsMatch(String seq, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 350 at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, PeptideDocNode nodePep, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 493 at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 466 at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 60 at pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings settings, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 79 at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable1 sequences, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 44 at pwiz.Skyline.Model.MassListImporter.MassListRowReader..ctor(IFormatProvider provider, Char separator, ColumnIndices indices, SrmSettings settings, IEnumerable1 sequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 615 at pwiz.Skyline.Model.MassListImporter.GeneralRowReader.Create(IList1 lines, IList1 headers, Int32 iDecoy, IFormatProvider provider, Char separator, SrmSettings settings, Int32 iirt, Int32 iLibrary) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 1164 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, ColumnIndices indices, IDictionary2 dictNameSeq, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 413 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 334 at pwiz.Skyline.Model.SrmDocument.ImportMassList(MassListInputs inputs, IProgressMonitor progressMonitor, IdentityPath to, IdentityPath& firstAdded, List1& irtPeptides, List1& librarySpectra, List1& errorList, List1& peptideGroups) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1075 at pwiz.Skyline.SkylineWindow.<>c__DisplayClass15b.<ImportMassList>b__14f(IProgressMonitor longWaitBroker) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1602 at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1587 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115 at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1600 at pwiz.Skyline.SkylineWindow.ImportMassList(String fileName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1576

[mvaudel]

Hi Moe,

When trying to open the file created in PeptideShaker it seems that it does not find a file. Please make sure that your mgf files are in the same folder as the mzid file. Also, this can happen whenever the file is on a server or a mapped drive like synced user folders. In general, try to keep files locally and if you have a synced/mapped user folder, avoid storing files there during processing.

Concerning the error with the OpenMS file, it seems like an incompatibility with the PTM annotation. I am not sure to which extend the tsv file is standardized and portable across libraries...

Hope this helps!

Best regards,

Marc

2016-01-10 23:53 GMT+01:00 1Moe notifications@github.com:

I'm starting to think something is not quite right with my pwiz. I've successfully converted a traml to tsv using TOPPAS. When I try to import this transition list csv file into skyline via import - transition lists I receive an error message.

Failed reading the file ...test.tsv. Unrecognized Unimod id 35 in modified peptide sequence

Below is more info. Would appreciate any help on this. regards, Moe

System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. ---> System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 277 at pwiz.Skyline.Model.ModificationMatcher.IsMatch(String seq, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 350 at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, PeptideDocNode nodePep, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 493 at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 466 at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 60 at pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings settings, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 79 at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable1 sequences, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 44 at pwiz.Skyline.Model.MassListImporter.MassListRowReader..ctor(IFormatProvider provider, Char separator, ColumnIndices indices, SrmSettings settings, IEnumerable1 sequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 615 at pwiz.Skyline.Model.MassListImporter.GeneralRowReader.Create(IList1 lines, IList1 headers, Int32 iDecoy, IFormatProvider provider, Char separator, SrmSettings settings, Int32 iirt, Int32 iLibrary) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 1164 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, ColumnIndices indices, IDictionary2 dictNameSeq, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 413 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 334 at pwiz.Skyline.Model.SrmDocument.ImportMassList(MassListInputs inputs, IProgressMonitor progressMonitor, IdentityPath to, IdentityPath& firstAdded, List1& irtPeptides, List1& librarySpectra, List1& errorList, List1& peptideGroups) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1075 at pwiz.Skyline.SkylineWindow.<>cDisplayClass15b.b14f(IProgressMonitor longWaitBroker) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1602 at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1587 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115 at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1600 at pwiz.Skyline.SkylineWindow.ImportMassList(String fileName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1576

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170403114 .

[1Moe]

Thank you very much, Marc,

you've just solved my problem! I was storing all of the test files straight on my C:\ drive (not in a subfolder). Copying the mgf and mzid files into a subfolder (e.g. c:\test) allowed me to do the skyline mzid import to create a spectral library.

I tested the wiff file import in searchgui and it works very well, thanks for implementing that! Question, Would it be possible to implement qtofpeakpicker in Searchgui for peakpicking of tof data (wiff files)? Reason I'm asking is that I created two mgfs (one with qtofpeakpicker and the other one with msconvert within searchgui). I set the threshold count to 150 most intense. When comparing the mgf files I noticed that I get exactly 150 most intense ions per precursor when using the qtofpeakpicking method. However, I get varying numbers (sometimes less than 100) of most intense ions in the msconvert peakpicking in searchgui. I think this may be due to decimal places of the intensities. I also noticed that the intensities of qtofpeakpicker are about 10x higher for each ion compared to the intensities in msconvert from searchgui.

I did a bit of a crude test: When I run Searchgui with only Xtandem on both mgf files individually and compare peptideshaker outputs: mgf qtofpeakpicker: #PSMs = 1981, ID rate =17.8%, FDR PSMs = 0.96 %, FDR peptides = 0.95 %, FDR Proteins = 0% mgf msconvert from searchgui: #PSMs = 1878, ID rate 16.8%, FDR PSMs = 0.96 %, FDR peptides = 0.94 %, FDR Proteins = 0.86%

Downloadable wiff, mgf and peptideshaker files at (note, I deleted the previous files) https://drive.google.com/open?id=0BybCLLWRgDsUX2VTc0F1ZlpCMnM

Cheers Moe

On 11 January 2016 at 21:40, Marc Vaudel notifications@github.com wrote:

Hi Moe,

When trying to open the file created in PeptideShaker it seems that it does not find a file. Please make sure that your mgf files are in the same folder as the mzid file. Also, this can happen whenever the file is on a server or a mapped drive like synced user folders. In general, try to keep files locally and if you have a synced/mapped user folder, avoid storing files there during processing.

Concerning the error with the OpenMS file, it seems like an incompatibility with the PTM annotation. I am not sure to which extend the tsv file is standardized and portable across libraries...

Hope this helps!

Best regards,

Marc

2016-01-10 23:53 GMT+01:00 1Moe notifications@github.com:

I'm starting to think something is not quite right with my pwiz. I've successfully converted a traml to tsv using TOPPAS. When I try to import this transition list csv file into skyline via import - transition lists I receive an error message.

Failed reading the file ...test.tsv. Unrecognized Unimod id 35 in modified peptide sequence

Below is more info. Would appreciate any help on this. regards, Moe

System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. ---> System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 277 at pwiz.Skyline.Model.ModificationMatcher.IsMatch(String seq, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 350 at

pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, PeptideDocNode nodePep, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 493 at

pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 466 at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 60 at

pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings settings, MappedList2 defSetStatic, MappedList2 defSetHeavy) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 79 at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable1 sequences, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 44 at

pwiz.Skyline.Model.MassListImporter.MassListRowReader..ctor(IFormatProvider provider, Char separator, ColumnIndices indices, SrmSettings settings, IEnumerable1 sequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 615 at pwiz.Skyline.Model.MassListImporter.GeneralRowReader.Create(IList1 lines, IList1 headers, Int32 iDecoy, IFormatProvider provider, Char separator, SrmSettings settings, Int32 iirt, Int32 iLibrary) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 1164 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, ColumnIndices indices, IDictionary2 dictNameSeq, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 413 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 334 at pwiz.Skyline.Model.SrmDocument.ImportMassList(MassListInputs inputs, IProgressMonitor progressMonitor, IdentityPath to, IdentityPath& firstAdded, List1& irtPeptides, List1& librarySpectra, List1& errorList, List1& peptideGroups) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1075 at

pwiz.Skyline.SkylineWindow.<>cDisplayClass15b.b14f(IProgressMonitor longWaitBroker) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1602 at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1587 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115 at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1600 at pwiz.Skyline.SkylineWindow.ImportMassList(String fileName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1576

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170403114

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170467854 .

[mvaudel]

Hi Moe,

Good to hear that this solved your issue! We will look into improving the way we handle raw files from different vendors. I cannot give you any timeline on this because we have very limited workforce but we will keep you posted :)

Best regards,

Marc

2016-01-12 4:34 GMT+01:00 1Moe notifications@github.com:

Thank you very much, Marc,

you've just solved my problem! I was storing all of the test files straight on my C:\ drive (not in a subfolder). Copying the mgf and mzid files into a subfolder (e.g. c:\test) allowed me to do the skyline mzid import to create a spectral library.

I tested the wiff file import in searchgui and it works very well, thanks for implementing that! Question, Would it be possible to implement qtofpeakpicker in Searchgui for peakpicking of tof data (wiff files)? Reason I'm asking is that I created two mgfs (one with qtofpeakpicker and the other one with msconvert within searchgui). I set the threshold count to 150 most intense. When comparing the mgf files I noticed that I get exactly 150 most intense ions per precursor when using the qtofpeakpicking method. However, I get varying numbers (sometimes less than 100) of most intense ions in the msconvert peakpicking in searchgui. I think this may be due to decimal places of the intensities. I also noticed that the intensities of qtofpeakpicker are about 10x higher for each ion compared to the intensities in msconvert from searchgui.

I did a bit of a crude test: When I run Searchgui with only Xtandem on both mgf files individually and compare peptideshaker outputs: mgf qtofpeakpicker: #PSMs = 1981, ID rate =17.8%, FDR PSMs = 0.96 %, FDR peptides = 0.95 %, FDR Proteins = 0% mgf msconvert from searchgui: #PSMs = 1878, ID rate 16.8%, FDR PSMs = 0.96 %, FDR peptides = 0.94 %, FDR Proteins = 0.86%

Downloadable wiff, mgf and peptideshaker files at (note, I deleted the previous files) https://drive.google.com/open?id=0BybCLLWRgDsUX2VTc0F1ZlpCMnM

Cheers Moe

On 11 January 2016 at 21:40, Marc Vaudel notifications@github.com wrote:

Hi Moe,

When trying to open the file created in PeptideShaker it seems that it does not find a file. Please make sure that your mgf files are in the same folder as the mzid file. Also, this can happen whenever the file is on a server or a mapped drive like synced user folders. In general, try to keep files locally and if you have a synced/mapped user folder, avoid storing files there during processing.

Concerning the error with the OpenMS file, it seems like an incompatibility with the PTM annotation. I am not sure to which extend the tsv file is standardized and portable across libraries...

Hope this helps!

Best regards,

Marc

2016-01-10 23:53 GMT+01:00 1Moe notifications@github.com:

I'm starting to think something is not quite right with my pwiz. I've successfully converted a traml to tsv using TOPPAS. When I try to import this transition list csv file into skyline via import - transition lists I receive an error message.

Failed reading the file ...test.tsv. Unrecognized Unimod id 35 in modified peptide sequence

Below is more info. Would appreciate any help on this. regards, Moe

System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. ---> System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 277 at pwiz.Skyline.Model.ModificationMatcher.IsMatch(String seq, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 350 at

pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String

seq, PeptideDocNode nodePep, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line

493 at

pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String

seq, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line

466 at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 60 at

pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings

settings, MappedList2 defSetStatic, MappedList2 defSetHeavy) in

c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line

79 at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable1 sequences, MappedList2 defSetStatic, MappedList2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 44 at

pwiz.Skyline.Model.MassListImporter.MassListRowReader..ctor(IFormatProvider

provider, Char separator, ColumnIndices indices, SrmSettings settings, IEnumerable1 sequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 615 at pwiz.Skyline.Model.MassListImporter.GeneralRowReader.Create(IList1 lines, IList1 headers, Int32 iDecoy, IFormatProvider provider, Char separator, SrmSettings settings, Int32 iirt, Int32 iLibrary) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 1164 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, ColumnIndices indices, IDictionary2 dictNameSeq, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 413 at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, List1& irtPeptides, List1& librarySpectra, List1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 334 at pwiz.Skyline.Model.SrmDocument.ImportMassList(MassListInputs inputs, IProgressMonitor progressMonitor, IdentityPath to, IdentityPath& firstAdded, List1& irtPeptides, List1& librarySpectra, List1& errorList, List1& peptideGroups) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1075 at

pwiz.Skyline.SkylineWindow.<>cDisplayClass15b.b14f(IProgressMonitor

longWaitBroker) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1602 at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1587 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115 at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1600 at pwiz.Skyline.SkylineWindow.ImportMassList(String fileName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1576

— Reply to this email directly or view it on GitHub <

https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170403114

.

— Reply to this email directly or view it on GitHub < https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170467854

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/94#issuecomment-170773644 .

[hbarsnes]

Hi Simion,

PeptideShaker now supports pepXML as an export option (via Export > Follow Up Analysis). It is still in a beta state, but it would be great if you could test it to see if it gives you want to need for your pipeline?

And as this issue has gotten too long and rather fragmented, I will now close it. So if the pepXML export does not work for you it would be great if you could open a new issue with the details? (But if it does work, it would also be great if you could let us know simply by replying to this (closed) issue?)

Best regards, Harald