A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2026-02-27, 16:44 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data_temp
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, DIA-NN, FragPipe, and nf-core/mhcquant.https://github.com/bigbio/pmultiqc
Results Overview
General Statistics
General statistics from the mhcquant pipeline.
| Sample Name | # Peptides | # Modified Peptides | # Proteins | # PSMs | # Epicores |
|---|---|---|---|---|---|
| PBMC007_B | 3632 | 248 | 2669 | 23195 | 3493 |
| PBMC009_A | 5652 | 265 | 3901 | 40350 | 5396 |
Identification Summary
Distribution of peptide lengths
This plot shows the distribution of peptide sequence lengths to assess variability and typical length ranges.
Created with MultiQC
Search Engine Scores
Percolator q-value Histogram
A q-value histogram in Percolator visualizes q-value distributions for PSMs, helping set the FDR threshold (typically 1%). It ensures only high-confidence identifications are retained, with a sharp drop-off beyond the threshold.
Created with MultiQC
Comet Xcorr Distribution
The Comet Xcorr boxplot visualizes the cross-correlation (Xcorr) score distribution for PSMs, indicating match quality. Higher Xcorr values signify better peptide-spectrum matches. This helps set a threshold to filter out low-confidence identifications.
Created with MultiQC
Median Feature Weights
For each feature, the associated weight is the median value calculated over all input samples.
The bar plot illustrates the median weights for each feature, which have been assigned to categories based on their source (e.g. psm_file, ms2pip, deeplc, im2deep).
Quantification Analysis
Peptide Intensity Distribution
Comparison of log2-transformed peptide intensities across samples. Helps assess data consistency and detect potential outliers or batch effects.
Created with MultiQC
MS1 Analysis
MS1 Chromatogram
An MS1 chromatogram is a plot of the intensity of precursor ions (MS1) detected over time, typically with retention time (RT) on the x-axis and ion intensity on the y-axis. It represents the total ion current (TIC) from the MS1 scan, which is useful for monitoring the overall elution profile of compounds during a chromatographic separation.
Created with MultiQC
Mass-to-Charge Histogram
This plot displays the distribution of precursor ion mass-to-charge (m/z) values detected in the dataset. It helps identify the typical m/z ranges and assess the overall coverage and instrument performance during acquisition.
Created with MultiQC
Mass Error Trends
Fragment mass error
The fragment mass error describes the differences between observed and theoretical fragment ion masses. It helps assessing the accuracy and calibration of the mass spectrometer by visualizing the error range and potential deviations. Depending on your configurations this error is plotted in Dalton (Da) or parts-per-million (ppm).
Created with MultiQC
RT Quality Control
Retention time Histogram
This plot shows the distribution of peptide retention times across the chromatographic gradient. It provides insight into peptide elution profiles and helps assess gradient performance and sample complexity.
Created with MultiQC
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| EASYPQP_CONVERT | easypqp | 0.1.53 |
| EASYPQP_LIBRARY | easypqp | 0.1.53 |
| EPICORE | epicore | 0.1.7 |
| MS2RESCORE | MSĀ²Rescore | 3.1.5) |
| OPENMSTHIRDPARTY_COMETADAPTER | Comet | 2024.01 rev. 1 |
| CometAdapter | 3.4.1 | |
| OPENMS_DECOYDATABASE | openms | 3.4.1 |
| OPENMS_FEATUREFINDERIDENTIFICATION | openms | 3.4.1 |
| OPENMS_FEATURELINKERUNLABELEDKD | openms-thirdparty | 3.4.1 |
| OPENMS_IDCONFLICTRESOLVER | openms | 3.4.1 |
| OPENMS_IDFILTER_QUANT | openms | 3.4.1 |
| OPENMS_IDFILTER_Q_VALUE | openms | 3.4.1 |
| OPENMS_IDMASSACCURACY | OpenMS | 3.4.1 |
| OPENMS_IDMERGER | openms | 3.4.1 |
| OPENMS_IDMERGER_QUANT | openms | 3.4.1 |
| OPENMS_IDRIPPER | openms | 3.4.1 |
| OPENMS_IDSCORESWITCHER | openms | 3.4.1 |
| OPENMS_MAPALIGNERIDENTIFICATION | openms | 3.4.1 |
| OPENMS_MAPRTTRANSFORMERIDXML | openms | 3.4.1 |
| OPENMS_MAPRTTRANSFORMERMZML | openms | 3.4.1 |
| OPENMS_MZTABEXPORTER | openms | 3.4.1 |
| OPENMS_PEPTIDEINDEXER | openms | 3.4.1 |
| OPENMS_PERCOLATORADAPTER | PercolatorAdapter | 3.4.1-pre-exported-20250822 |
| percolator | 3.07.1, Build Date Mar 13 2025 17:19:27 | |
| OPENMS_PSMFEATUREEXTRACTOR | openms | 3.4.1 |
| OPENMS_TEXTEXPORTER | openms | 3.4.1 |
| PYOPENMS_CHROMATOGRAMEXTRACTOR | pyopenms | 3.4.1 |
| PYOPENMS_IONANNOTATOR | pyopenms | 3.4.1 |
| SUMMARIZE_RESULTS | pyopenms | 3.4.1 |
| THERMORAWFILEPARSER | thermorawfileparser | 1.4.5 |
| Workflow | Nextflow | 25.10.2 |
| nf-core/mhcquant | v3.1.0-gf704fa3 |