Can PeptideShaker outputs be used for OpenSWATH analysis?

[Pratik Jagtap]

Hello Marc,

Please see attached slides that Sarah made. This might give an overview and also multipe entry points into the OpenSWATh workflow.

Can you please take a look at Slides (in particular 2 and 3) and see if there are any opportunities for integrating PeptideShaker outputs with OpenSWATH workflow?

• Can PeptideShaker be seen as an alternative (to TPP tools) either to generate any of the intermediate steps or as an input for SpectraST?

• Can mzidentml be converted to pepxml?

Ira - Here is an example for mzidentml file generated through PeptideShaker. Would you like to try it through idconvert?

https://netfiles.umn.edu/xythoswfs/webview/_xy-17245417_1

• Can PeptideShaker generate a .traml file?

Regards,

Pratik

On Fri, Feb 6, 2015 at 5:29 AM, Gmail <irac...@gmail.com> wrote:

Hi Marc

Yes totally true. It would likely be a good start and then usually some kind of "fixing" is sure to be required

Cheers

Ira

Sent from my iPhone

On 6 Feb 2015, at 9:30 pm, Marc Vaudel <mva...@gmail.com> wrote:

Hi Ira,

That is a good idea, but you might want to test whether the pepxml file generated by idconvert is compatible with SpectraST - ie is the PeptideProphet/iProphet flavor of pepxml, with indexes, charges, PTMs and PEPs annotated accordingly.

Best regards,

Marc

2015-02-06 11:15 GMT+01:00 Ira Cooke <irac...@gmail.com>:

Hi All, 

I'm not sure if I'm following exactly, but could idconvert (from proteowizard) be a solution here?  It can do mzid to pepxml conversion.

Cheers

Ira

On 6 Feb 2015, at 9:08 pm, Marc Vaudel <mva...@gmail.com> wrote:

Hi Sarah,

Thank you for your quick answer. Do you by any chance plan to implement the conversion from mzIdentML too? If this is not an option note that we could generate TraML files directly if you provide us with the information needed for this. This sounds to me like a much more generic solution and not more work than pepXML.

Best regards,

Marc

On Thu, Feb 5, 2015 at 3:07 PM, Sarah Parker <spar...@gmail.com> wrote:

Hello Marc,

The pep.xml is needed in the established version we have for building an assay library for openSWATH to read and use to extract and identify peptides from the DIA files. For that workflow, there are already scripts to convert SpectraST library files into the .TraML file format needed for openSWATH analysis. An alternative tool could be built to convert a library other than SpectraST into the right format, it's just that we already have the tools to work with SpectraST so it's a lower hanging fruit. As long as we can convert any search result into the pep.XML format it can be incorporated into spectrast.

Does that help?

Sarah

On Thu, Feb 5, 2015 at 2:52 PM, Marc Vaudel <mva...@gmail.com> wrote:

Dear Pratik,

After digging a bit more in the documentation it seems that there is no alternative to a PeptideProphet-like pepXML file. Would you by any chance have such a file at hand?

I must say I don't get the connection with OpenSWATH? Is there a way to connect both software? Sorry, I am not familiar with these tools :)

Best regards,

Marc

2015-02-03 19:18 GMT+01:00 Pratik Jagtap <pja...@umn.edu>:

Thanks for your answer.

> However, I see that SpectraST supports simple text input, we can implement such an export very easily. I will contact the developers on this.

This would be great. We would really look forward to this functionality as we are looking at using OpenSWATH workflow within Galaxy.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

On Tue, Feb 3, 2015 at 11:11 AM, Marc Vaudel <mva...@gmail.com> wrote:

Dear Pratik,

We implemented the SWATH report for a user who was using it as input in a manufacturer (AB) tool directly, and according to the manufacturer specifications. However, due to the lack of documentation of this export, and the absence of support from the manufacturer, we were never able to get this file in the software... 

Now as far as I heard from users, the best results in DIA are obtained when combining PeptideShaker with Skyline. The best for this would be to use mzIdentML export but the support in Skyline is not ready (you can follow the progress on this thread https://brendanx-uw1.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=18964 - and eventually post to get us higher in the todolist ;) ).

I would stay away from the pepxml format because it is not well designed to store identification results. As a results the different implementations have different hacks around the format shortcomings, and we might run into compatibility issues there. We are encountering these when taking pepxml as input and would be happy to stay away from these for our output :) However, I see that SpectraST supports simple text input, we can implement such an export very easily. I will contact the developers on this.

Best regards,

Marc

2015-02-03 17:01 GMT+01:00 Pratik Jagtap <pja...@umn.edu>:

Hello Marc and Harald,

I have two questions related to PeptideShaker :

a) In one of the release notes, we noticed that there is a beta version of SWATH report that PeptieShaker can generate. Can this export be used as an input (along with pepxml file) for SpectraST? Which software would use this report?

Changes in PeptideShaker 0.25.0 (February 4. 2014)

• NEW FEATURE: Added a simple swath export.

b) Do you know of any tool that can generate a pepxml report from a mzidentml file?

Thanks and Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

[Marc Vaudel]

Hi Pratik,

From your charts it seems that you can use PeptideShaker for the DDA part. In order to chain it with OpenSWATH we can either use the mzIdentML to pepXML to TraML conversion option, or the direct output of TraML. The latter sounds less prone to issues but will result in more work on our side. Maybe the former can be used as preliminary solution while we implement the direct export of TraML from PeptideShaker?

Best regards,

Marc

[Pratik Jagtap]

Hello Marc,

Yes, I agree we will try the mzidentML to pepXML to TraML option with the first install. Direct export of TraML can be used in a later version.

Thanks,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[harald.barsnes]

 

Hi Sarah,

 

I'm not an expert on idconvert, but I can tell you that the CV term it is complaining about is MS:1002458, which is the CV term for PeptideShaker. We only use this once as part of the SoftwareName tag in the AnalysisSoftware section.

 

My guess is that idconvert would have to be extended to support mzIdentML files from PeptideShaker. I assume they depend on the software used when parsing the mzIdentML file. The rest of the content should be pretty standard though, so it shouldn't be too difficult.

 

We're having the same discussion with the Skyline developers btw (https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=18964).

 

Best regards,

Harald

[Marc Vaudel]

Hi Sarah,

The ProteoWizard are generally very helpful and responsive. I am sure they will be very quick at updating their code to support the new CV terms :) This also sounds like the best solution on the long term for both sides :)

Best regards,

Marc

2015-02-10 19:46 GMT+01:00 Sarah Parker <spar...@gmail.com>:

Hi Harald, thank you for that informative response,

There seem to be two solutions:

1) adapt 'idconvert' to read the mzID files from PeptideShaker or

2) re-format the mzID file to be readable to idconvert

Which of these seem the most feasible for us?

Thanks,

Sarah

[Pratik Jagtap]

Thanks Marc,

Marc or Ira - do you know anyone at ProteoWizard that we can contact and have the code updated?

Thanks,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

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[Pratik Jagtap]

> I’m currently away on leave and don’t have easy access to an example peptideshaker mzid file, but Sarah Parker or Harald Barsnes (cc’ed) can probably send you one if you would like one to experiment with.

Hello Matt - please see if the following mzid file can be used for analyses.

https://netfiles.umn.edu/xythoswfs/webview/_xy-17245430_1

Sarah found the following error:

parkers@node1083 [~] % idconvert test_mzident_peptideshaker.mzid --pepXML

format: pepXML

outputPath: .

extension: .pepXML

filenames:

  test_mzident_peptideshaker.mzid

  

processing file: test_mzident_peptideshaker.mzid

Invalid cvParam accession "1002458"

Error processing file test_mzident_peptideshaker.mzid

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

On Tue, Feb 10, 2015 at 6:50 PM, Ira Cooke <I.C...@latrobe.edu.au> wrote:

Dear Matt,

We are hoping to use idconvert to convert mzid files produced by peptideshaker to pepXML.  It looks like there are some CV terms that idconvert doesn’t recognise.  Hopefully these can be added into the next Proteowizard release?  

I’m currently away on leave and don’t have easy access to an example peptideshaker mzid file, but Sarah Parker or Harald Barsnes (cc’ed) can probably send you one if you would like one to experiment with.

Best wishes

Ira

-------------------------------------------------

Dr Ira Cooke
Life Sciences Computation Centre, 
Department of Biochemistry
La Trobe University,
Phone +61 (3) 94792256

Mobile: 0429105999
Email: i.c...@latrobe.edu.au