Need help in doing proteomics analysis

Question

[rishav513]

Hello everyone. Greetings of the day.

I need help in doing proteomics analysis.

I have MaxQuant output files that contain files :
aifMsms.txt, allPeptides.txt, evidence.txt, modificationSpecificPeptides.txt, msms.txt, msmsScans.txt, msScans.txt, mzRange.txt, Oxidation (M)Sites.txt, parameters.txt, peptides.txt, proteinGroups.txt, simPeptides.txt, simScans.txt, summary.txt .
I don't understand how to further perform differential expression analysis in R through these files. 

I am new to proteomics analysis. So, any help would be appreciated.

Answer 1

[ATpoint]

Bioconductor has several packages starting from MaxQuant with extensive manuals that guide your through the DE endeavour, e.g.:

https://www.bioconductor.org/packages/release/bioc/vignettes/DEqMS/inst/doc/DEqMS-package-vignette.html

https://bioconductor.org/packages/release/bioc/vignettes/DEP/inst/doc/DEP.html

Answer 2

[cpad0112]

you can also consider galaxy for the same. Here are tutorials:

1. https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html
2. https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/tutorial.html