nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
1.2.0
). The latest
stable release is
2.6.0
.
Output
This document describes the output produced by the pipeline
Pipeline overview
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
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.
csv
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.