I was given a data set consisting of 6 samples: 3 control and 3 treated. 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

These are data generated by the PEAKS Studio. The software should include a quantification feature. If your samples were run through an HRMS then you can run LFQ with PEAKS.