Identify and quantify MHC eluted peptides from mass spectrometry raw data
This document describes the output produced by the pipeline
The final output of the pipeline should include the following files:
- mzTab - the community standard format for sharing mass spectrometry search results
- csv - aggregate csv report, containing all information about peptide identification and quantification results
mzTab is a light-weight format to report mass spectrometry search results. It provides all important information about idenfied peptide hits and is compatible with the PRIDE Archive - proteomics data repository.
The csv output file is a table containing all information extracted from a database search throughout the pipeline. See the OpenMS or PSI documentation for more information about annotated scores and format (http://ftp.mi.fu-berlin.de/pub/OpenMS/release1.9-documentation/html/TOPP_TextExporter.html).
Each row index is represented by a label describing its content:
#MAP contains information about the different mzML files that were provided initially
#RUN contains information about the search that was performed on each run
#PROTEIN contains infomration about the protein ids corresponding to the peptides that were detected (No protein inference was performed)
#UNASSIGNEDPEPTIDE contains information about PSMs that were identified but couldn’t be quantified to a precursor feature on MS Level 1
#CONSENSUS contains information about precursor features that were identified in multiple runs (eg. run 1-3 in this case)
#PEPTIDE contains information about peptide hits that were identified and correspond to the consensus features described one row above.