Identify and quantify MHC eluted peptides from mass spectrometry raw data
This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
The pipeline is built using Nextflow and processes data using the following steps:
- Class prediction
- Rotation time prediction
- Workflow reporting and documentation
--skip_quantificationis not specified.
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.
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 information 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 below
--refine_fdr_on_predicted_subsetis specified, consists of the hits (filtered by q-value)
*.mztab: mztab file generated by the OpenMS MzTabExporter command, the community standard format for sharing mass spectrometry search results
--skip_quantificationis not specified, then this file is generated by the OpenMS FeatureFinderIdentification command
--skip_quantificationis not specified, then this file is generated by the OpenMS IDFilter command
*all_ids_merged_psm_perc*.idXML: idXML files are generated when
--refine_fdr_on_predicted_subsetis specified, then this file consists of the PSMs prediction outcome
--refine_fdr_on_predicted_subsetis specified, then this file is the outcome of the second percolator run, generated by the OpenMS PercolatorAdapter
This folder contains the intermediate results from various steps of the MHCquant pipeline (e.g. (un)filtered PSMs, aligned mzMLs, features)
The output mzTab contains many columns annotating the most important information - here are a few outpointed:
Most important to know that in this format we annotated the q-value of each peptide identification in the
best_seach_engine_score column and peptide quantities in the peptide_abundance_study_variable` columns.
mzTab is a light-weight format to report mass spectrometry search results. It provides all important information about identified peptide hits and is compatible with the PRIDE Archive - proteomics data repository.
--include_proteins_from_vcfis specified, then this fasta is created for the respective sample
These CSV files list all of the theoretically possible neoepitope sequences from the variants specified in the vcf and neoepitopes that are found during the mass spectrometry search, independant of binding predictions, respectively
*found_neoepitopes_class1.csv: Generated when
*found_neoepitopes_class2.csv: Generated when
This CSV which lists all neoepitopes that are found during the mass spectrometry search, independant of binding predictions The format is as follows:
*vcf_neoepitopes_class1.csv: Generated when
*vcf_neoepitopes_class2.csv: Generated when
This CSV fils contains all theoretically possible neoepitope sequences from the variants that were specified in the vcf The format is shown below
Class (1|2) bindings
--predict_class_1is specified, then this CSV is generated
--predict_class_2is specified, then this CSV is generated
This folder containing the binding predictions of all detected class 1 or 2 peptides and all theoretically possible neoepitope sequences The prediction outputs are comma-separated table (CSV) for each allele, listing each peptide sequence and its corresponding predicted affinity scores:
Rotation time prediction
--predict_RTis specified, the rotation time found peptides are provided
--predict_RTis specified, the rotation time predicted neoepitopes are provided
multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
multiqc_plots/: directory containing static images from the report in various formats.
MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.
- Reports generated by Nextflow:
- Reports generated by the pipeline:
pipeline_report*files will only be present if the
--email_on_failparameter’s are used when running the pipeline.
- Reformatted samplesheet files used as input to the pipeline:
- Reports generated by Nextflow:
Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.