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I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent.

Each sample corresponds to a folder within which there are the following files:

"DB search psm.csv" "de novo only peptides.csv" "de novo only peptides.xml" "de novo only spectra.mgf" "filter.csv" "peptide features.csv" "peptide.csv" "peptides_1_1_0.mzid" "peptides.pep.xml" "protein-peptides.csv" "proteins.csv" "proteins.fasta" "PSM ions.csv"

The "peptide.csv" files have the following column names:

Peptide -10lgP Mass Length ppm m/z RT 1/k0 Range Area Ctrl-2 Fraction Precursor Id Source

The "proteins.csv" files have the following column names:

Protein Group Protein ID Accession -10lgP Coverage (%) Coverage (%) Ctrl-1 Area Ctrl-1 #Peptides #Unique #Spec Ctrl-1 PTM Avg. Mass Description

Has anybody ever worked with these type of data?

I would like to do exploit these data and perform a differential analysis but i don't know how to create a SummarizedExperiment from these data.

Any help would be greatly appreciated.

Thank you

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Sep 8, 2022 at 16:39
  • $\begingroup$ Could you provide an example dataset? And post the headers and top 5 rows of each file? $\endgroup$
    – Soerendip
    Jan 12, 2023 at 12:59

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