Question

R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?

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mmvar • 0

@d9340be0

Last seen 9 months ago

Portugal

I am trying to read into R a .mzid file using the readPSMs() function of the PSMatch package. This file was exported from the ProteinPilot software (Sciex) after searching 4 raw files (.wiff) of DDA data against a sequence database obtained from UniProt. After reading it into R with the PSMatch package the following error message appears:

Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in as_data_frame(mzR::openIDfile(f)): identical(iddf[, 1], scores[, 1]) is not TRUE

It seems to work fine with other .mzid files obtained from ProteomeXchange. What am I doing wrong?

RforProteomics Proteomics ProteomicsWorkflow • 1.1k views

ADD COMMENT • link updated 15 months ago by Laurent Gatto 1.6k • written 15 months ago by mmvar • 0

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I don't think you are doing anything wrong. The mzR::openIDfile() function does some extra checks and one of them fails. This is possibly related to ProteinPilot export. You could try to change the importer parser to "mzID".

ADD REPLY • link 15 months ago Laurent Gatto 1.6k

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Also, make sure you set the import arguments right - check (and use) the PSM() manual page.

ADD REPLY • link 15 months ago Laurent Gatto 1.6k

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I tried changing the parser but it didn't work. The error message is different though.

Input:

ppid <- PSM("D:/MiguelRosado/Bioconductor/R_for_MS_Proteomics/R_for_MS_Proteomics/Data/PAC/DDA/ProteinPilot/AD_IDA1.mzid",
        parser = "mzID")

Output:

reading AD_IDA1.mzid...Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'flatten': Version 1.2 unknown: only 1.0 and 1.1 supported.

It seems I have an unsupported version of.. something.. I don't know what.

ADD REPLY • link 15 months ago mmvar • 0

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One thing that comes to mind is that ProteinPilot exports search results in mzIdentML version 1.2. Is this incompatible with PSMatch?

ADD REPLY • link 15 months ago mmvar • 0

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mzID seems to struggle, indeed.

You could test if the version is an issue with

mzR::openIDfile("AD_IDA1.mzid")

(see ?openIDfile from mzR for details)

If that works, check that the import arguments in ?PSM.

I'm happy to look into it by the end of August. Not sure I'll have time before.

ADD REPLY • link 15 months ago Laurent Gatto 1.6k