Import MaxQuant result into Peptide-Shaker

Jiancheng Ding

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Jun 16, 2020, 3:25:36 AM6/16/20

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Is there a guideline on how to import maxquant result in to Peptide?

Or how to convert maxquant result to Peptide-Shaker format?

matte...@libero.it

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Jun 16, 2020, 5:03:56 AM6/16/20

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HELLO I CAN ASK YOU ONE THING ON HOW TO TRANSFORM RAW DATA

Il 16 giugno 2020 alle 9.25 Jiancheng Ding <d33...@gmail.com> ha scritto:

Is there a guideline on how to import maxquant result in to Peptide?
Or how to convert maxquant result to Peptide-Shaker format?

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Jiancheng Ding

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Jun 16, 2020, 9:14:34 PM6/16/20

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It seems that there is a Thermo Raw File Reader

On Tuesday, June 16, 2020 at 5:03:56 PM UTC+8, matte...@libero.it wrote:

HELLO I CAN ASK YOU ONE THING ON HOW TO TRANSFORM RAW DATA

Il 16 giugno 2020 alle 9.25 Jiancheng Ding <d33...@gmail.com> ha scritto:

Is there a guideline on how to import maxquant result in to Peptide?
Or how to convert maxquant result to Peptide-Shaker format?

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You received this message because you are subscribed to the Google Groups "PeptideShaker" group.

To unsubscribe from this group and stop receiving emails from it, send an email to peptide...@googlegroups.com.

Harald Barsnes

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Jun 17, 2020, 9:16:17 AM6/17/20

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Hi,

At the moment I am afraid that there is no support for importing MaxQuant results into PeptideShaker. But given that MaqQuant is focused on quantification and PeptideShaker on identification the gains would be minimal I think?

You may however run the MaqQuant search engine called Andromeda via SearchGUI and import those results into PeptideShaker.

Best regards,

Harald

Harald Barsnes

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Jun 17, 2020, 9:21:32 AM6/17/20

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Hi,

If you have Thermo raw files you can use either ThermoRawFileParser (command line: https://github.com/compomics/ThermoRawFileParser, or graphical user interface: https://github.com/compomics/ThermoRawFileParserGUI) or ProteoWizard (http://proteowizard.sourceforge.net). If you have other raw files formats, ProteoWizard would be your tool.

For more details on how to use the tools you can check out our tutorial material: https://www.compomics.com/bioinformatics-for-proteomics. See chapter 1.2 Peak List Generation.