QC Metrics Reference¶

This page lists all quality control metrics computed by pmultiqc, organized by data level. Each metric includes a description, the source file(s) it is derived from, and the modules that produce it.

PSM-Level Metrics¶

Metric	Description	Source	Modules
PSM Count	Total number of peptide-spectrum matches passing FDR	mzTab, evidence.txt, report.tsv	quantms, maxquant, diann
MS/MS Identification Rate	Percentage of MS2 spectra matched to a peptide	summary.txt, mzTab	quantms, maxquant
Search Engine Score	Distribution of PSM-level confidence scores (e.g., Andromeda score, OpenMS score)	idXML, msms.txt	quantms, maxquant
Delta Mass (Da)	Difference between experimental and theoretical precursor mass in daltons	mzTab, evidence.txt, mzid	quantms, maxquant, mzidentml
Delta Mass (ppm)	Mass error expressed in parts per million; calibrated vs. uncalibrated	mzTab, evidence.txt	quantms, maxquant
Precursor Charge State	Frequency of +1, +2, +3, +4, +5, +6+ charge states among identified PSMs	mzTab, evidence.txt, report.tsv, mzid	all
Retention Time Distribution	Histogram of PSM identification times across the LC gradient	mzTab, evidence.txt	quantms, maxquant, mzidentml
Oversampling	Fraction of precursors fragmented more than once in a single run	evidence.txt, mzML	quantms, maxquant, mzidentml

Peptide-Level Metrics¶

Metric	Description	Source	Modules
Peptide Count	Total unique peptide sequences identified per sample	mzTab, evidence.txt, report.tsv	all
Missed Cleavages	Distribution of peptides with 0, 1, or 2 missed tryptic cleavage sites	mzTab, evidence.txt	quantms, maxquant
Peptide Length Distribution	Histogram of peptide sequence lengths (number of amino acid residues)	mzTab, evidence.txt, report.tsv	quantms, maxquant, diann
Peptide Intensity	Log2-transformed peptide-level signal intensity per sample	mzTab, evidence.txt	quantms, maxquant
Missing Values (Peptide)	Fraction of peptides with no quantification value in a given sample	mzTab	quantms
Modifications	Summary of variable modifications identified (phospho, oxidation, etc.)	mzTab, evidence.txt	quantms, maxquant
Peptide Table	First 500 peptides with identification scores and quantification values	mzTab	quantms

Protein-Level Metrics¶

Metric	Description	Source	Modules
Protein Group Count	Total unique protein groups identified per sample	mzTab, proteinGroups.txt, report.tsv	all
Peptides per Protein	Distribution of unique peptide counts assigned to each protein group	mzTab, proteinGroups.txt	quantms, maxquant, diann, mzidentml
Protein Identification Summary Table	Per-sample table with PSM, peptide, and protein counts	mzTab, proteinGroups.txt	quantms, maxquant
Contaminant Fraction	Percentage of total protein signal attributable to common contaminants	proteinGroups.txt, mzTab	quantms, maxquant, fragpipe
Top N Contaminants	Ranked list of the most abundant contaminant proteins detected	mzTab, proteinGroups.txt	quantms, maxquant
Protein Quantification Table	LFQ, iBAQ, or TMT intensities per protein group across conditions	mzTab, proteinGroups.txt	quantms, maxquant

MS1-Level Metrics¶

Metric	Description	Source	Modules
Total Ion Chromatogram (TIC)	Sum of all ion intensities at each retention time point	mzML	quantms, diann, mzidentml
Base Peak Chromatogram (BPC)	Intensity of the most abundant ion at each retention time point	mzML	quantms, diann, mzidentml
MS1 Scan Count	Total number of survey (MS1) scans per raw file	mzML, ms_info.tsv	quantms, diann
MS2 Scan Count	Total number of fragmentation (MS2) scans per raw file	mzML, ms_info.tsv	quantms, diann

MS2-Level Metrics¶

Metric	Description	Source	Modules
Peaks per MS2 Spectrum	Histogram of fragment ion peak counts per spectrum	mzML, mgf	quantms, maxquant, mzidentml, diann
Peak Intensity Distribution	Distribution of MS2 fragment ion intensities (log scale)	mzML, mgf	quantms, maxquant, mzidentml, diann

Experimental Design and Sample-Level Metrics¶

Metric	Description	Source	Modules
Experimental Design Table	Sample-to-file mapping with biological replicate, fraction, and technical replicate	experimental_design.tsv, sdrf.tsv	quantms, maxquant, diann
Sample Correlation Heatmap	Pairwise sample correlation matrix based on peptide/protein intensities	mzTab, proteinGroups.txt	quantms, maxquant
ID Rate over RT	Identification rate binned by retention time; normalized per run	mzML + mzTab	quantms, mzidentml

ProteoBench-Specific Metrics¶

Metric	Description	Source
Log2 Mean Intensity	Mean log2 intensity per precursor, split by Condition A and B	result_performance.csv
Coefficient of Variation (CV)	Intra-condition CV of precursor intensities	result_performance.csv
Log2 Fold Change (A vs. B)	Observed fold change between two conditions	result_performance.csv
Epsilon	Deviation of observed from expected log2 fold change	result_performance.csv
Missing Value Count	Number of precursors without intensity in each condition	result_performance.csv
Intensity per File	Per-run precursor counts and intensity distributions	result_performance.csv

mhcquant-Specific Metrics¶

Metric	Description	Source
m/z Histogram	Distribution of precursor m/z values	multiqc_histogram_mz.txt
RT Histogram	Distribution of peptide retention times	multiqc_histogram_rt.txt
Ion Mobility Histogram	Distribution of ion mobility values (Bruker timsTOF)	multiqc_histogram_im.txt
Score Histogram	Distribution of PSM identification scores	multiqc_histogram_scores.txt
Xcorr Scores	Sequest cross-correlation score distribution	multiqc_scores_xcorr.txt
Mass Error	Mass accuracy histogram for identified MHC peptides	multiqc_mass_error.txt
Peptide Intensity	Quantification signal distribution for MHC-bound peptides	multiqc_peptide_intensity.txt
Percolator Output	Post-processing score distribution from Percolator	percolator_plot.txt
Peptide Length Distribution	Sequence length histogram (MHC-I: 8–11 aa; MHC-II: 13–25 aa)	multiqc_length_dist.txt