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.
Quantification<details markdown="1"> <summary>Output files</summary>
--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
#MAP id filename label size
RUN contains information about the search that was performed on each run
#RUN run_id score_type score_direction date_time search_engine_version parameters
PROTEIN contains information about the protein ids corresponding to the peptides that were detected (No protein inference was performed)
#PROTEIN score rank accession protein_description coverage sequence
UNASSIGNEDPEPTIDE contains information about PSMs that were identified but couldn't be quantified to a precursor feature on MS Level 1
#UNASSIGNEDPEPTIDE rt mz score rank sequence charge aa_before aa_after score_type search_identifier accessions FFId_category feature_id file_origin map_index spectrum_reference COMET:IonFrac COMET:deltCn COMET:deltLCn COMET:lnExpect COMET:lnNumSP COMET:lnRankSP MS:1001491 MS:1001492 MS:1001493 MS:1002252 MS:1002253 MS:1002254 MS:1002255 MS:1002256 MS:1002257 MS:1002258 MS:1002259 num_matched_peptides protein_references target_decoy
CONSENSUS contains information about precursor features that were identified in multiple runs (eg. run 1-3 in this case)
#CONSENSUS rt_cf mz_cf intensity_cf charge_cf width_cf quality_cf rt_0 mz_0 intensity_0 charge_0 width_0 rt_1 mz_1 intensity_1 charge_1 width_1 rt_2 mz_2 intensity_2 charge_2 width_2 rt_3 mz_3 intensity_3 charge_3 width_3
PEPTIDE contains information about peptide hits that were identified and correspond to the consensus features described below
#PEPTIDE rt mz score rank sequence charge aa_before aa_after score_type search_identifier accessions FFId_category fea
Intermediate results<details markdown="1"> <summary>Output files</summary>
--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:
PEP sequence accession best_search_engine_score retention_time charge mass_to_charge peptide_abundance_study_variable
Most important to know is that in this format we annotated the q-value of each peptide identification in the
best_search_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.
Reference fasta<details markdown="1"> <summary>Output files</summary>
--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<details markdown="1"> <summary>Output files</summary>
\*found_neoepitopes_class1.csv: Generated when
\*found_neoepitopes_class2.csv: Generated when
This CSV lists all neoepitopes that are found during the mass spectrometry search, independant of binding predictions.
The format is as follows:
peptide sequence geneID
vcf_neoepitopes<details markdown="1"> <summary>Output files</summary>
\*vcf_neoepitopes_class1.csv: Generated when
\*vcf_neoepitopes_class2.csv: Generated when
This CSV file contains all theoretically possible neoepitope sequences from the variants that were specified in the vcf.
The format is shown below
Sequence Antigen ID Variants
Class (1|2) bindings<details markdown="1"> <summary>Output files</summary>
--predict_class_1is specified, then this CSV is generated
--predict_class_2is specified, then this CSV is generated
This folder contains 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:
peptide allele prediction prediction_low prediction_high prediction_percentile
Retention time prediction<details markdown="1"> <summary>Output files</summary>
--predict_RTis specified, the retention time found peptides are provided
--predict_RTis specified, the retention time predicted neoepitopes are provided
MultiQC<details markdown="1"> <summary>Output files</summary>
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.
Pipeline information<details markdown="1"> <summary>Output files</summary>
- Reports generated by Nextflow:
- Reports generated by the pipeline:
pipeline_report\*files will only be present if the
--email_on_failparameters 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.