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SimionKreimer / mzidentML-to-pepXML-convert

Convert mzidentML result files to pepXML format
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How did you get searchGUI results to pep.xml for spectral libraries #1

Open sfghuis opened 7 years ago

sfghuis commented 7 years ago

Hi Simion,

I am currently trying to use searchGUI results for spectral library generation. This seems to be somewhat of a problem and based on your previous post you where able to solve this one! Could you please explain me how you did this? IDpicker and peptideshaker produce rather useless results in this case, I am trying to get openMS to work but I wondered if you found a different approach?

Kind regards, Bas

SimionKreimer commented 7 years ago

Hi Bas, I have struggled with this issue quiet a bit on my end, and I should take this script off of github since it was one of the first things I tried, which I believe didn't work out in the long run since IDconvert shuffled the spectrum reference numbers and thus made a useless library. There is currently an export to pepXML option in PeptideShaker, I believe, which should allow you to work with SpectraST to make a library. In my own case, I had our biostatistician put together a mzidentML parser which converts an mzidentML file to a TSV file that can be manipulated by OpenSWATH to make a library for DIA analysis (see the supplement of my paper: http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04892). The parser however doesn't scale well to complex samples, but I can share it with you once I dig it out of my archives. I would try the pepXML exporter first and if that fails take a look at the paper and you can try this parser if you like. Good luck, it's doable but requires a bit of elbow grease.

Best, Simion

sfghuis commented 7 years ago

Dear Simion,

Thank you for your reply! There is indeed such a function in peptideshaker but it only works for all files and i need the pep.xml for all file seperatly.

I would love to take a look at the parser, could you send the share link to sfgroothuis@Hotmail.com?

Kind regards

From: SimionKreimer notifications@github.com Sent: 30 May 2017 15:47 To: SimionKreimer/mzidentML-to-pepXML-convert Cc: sfghuis; Author Subject: Re: [SimionKreimer/mzidentML-to-pepXML-convert] How did you get searchGUI results to pep.xml for spectral libraries (#1)

Hi Bas, I have struggled with this issue quiet a bit on my end, and I should take this script off of github since it was one of the first things I tried, which I believe didn't work out in the long run since IDconvert shuffled the spectrum reference numbers and thus made a useless library. There is currently an export to pepXML option in PeptideShaker, I believe, which should allow you to work with SpectraST to make a library. In my own case, I had our biostatistician put together a mzidentML parser which converts an mzidentML file to a TSV file that can be manipulated by OpenSWATH to make a library for DIA analysis (see the supplement of my paper: http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04892). The parser however doesn't scale well to complex samples, but I can share it with you once I dig it out of my archives. I would try the pepXML exporter first and if that fails take a look at the paper and you can try this parser if you like. Good luck, it's doable but requires a bit of elbow grease.

Best, Simion

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