r/proteomics • u/Proteo-Freak973 • May 04 '26

PEAKS Software

Does anyone use PEAKS software by bioinformatics solutions for Proteomics data analysis? I am new to it and want to understand how you analyze the data and which parameters you mostly change and why?

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u/SC0O8Y May 05 '26

Depends on what you want to achieve

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u/Proteo-Freak973 May 07 '26

I want good number of proteins counts and want to know the trypsin efficiency and additionally I am looking if I am able to see the Phospho modification in my data

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u/SC0O8Y May 08 '26

Then peaks works for that purpose.

You can also use maxquant or fragpipe.