nf-core pipeline ·
nf-core/ribomsqc
A quality control pipeline that monitors mass spectrometer performance during ribonucleoside analysis.
What nf-core/ribomsqc is
nf-core/ribomsqc is an automated Nextflow pipeline designed to track and monitor mass spectrometer performance in ribonucleoside analysis. Originally written by Roger Olivella, the tool evaluates analytical reproducibility by measuring target nucleosides across experimental runs.
Ribonucleoside quantification and profiling rely on consistent mass spectrometry performance, where subtle drifts in mass accuracy or retention times can compromise data quality. The pipeline automates the extraction of key quality metrics from raw analytical data, producing consolidated reports that allow researchers to verify instrument behaviour and detect analytical anomalies.
What the pipeline does
The workflow ingests vendor RAW data files alongside a reference tab-separated values (TSV) table containing target compound specifications, including theoretical retention times, molecular ion masses (m/z), and fragment masses. RAW data files are converted using ThermoRawFileParser, after which extracted ion chromatograms (XIC) are generated using MSnbase according to user-configured retention time and m/z tolerance thresholds.
Extracted metrics are merged into JSON files and compiled into an integrated MultiQC report that summarises instrument performance, retention behaviour, and compound metrics across all samples.
Key facts
- Pipeline topic
- Ribonucleoside mass spectrometry quality control
- Original author
- Roger Olivella
- Version
- 1.0.0
- Primary inputs
- Thermo .raw files via samplesheet CSV, analytes TSV file
- Core tools
- ThermoRawFileParser, MSnbase, MultiQC
- Primary outputs
- MultiQC report, merged JSON metric files
What you can use it for
- Monitoring instrument stability
- Track mass spectrometer performance across analytical batches of ribonucleoside samples to detect instrument degradation or drift.
- Retention time deviation assessment
- Compare observed chromatographic retention times against defined theoretical values for specific ribonucleosides.
- Automated quality control reporting
- Generate interactive MultiQC visual reports aggregating chromatography and mass spectrometry metrics from multiple raw files.
Run it here
The research agent runs nf-core/ribomsqc with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Automates the end-to-end quality control workflow directly from raw mass spectrometer files.
- Integrates data into centralised MultiQC reports for rapid inspection across large sample batches.
- Allows user-defined adjustment of retention time tolerances, m/z tolerances, and MS acquisition levels.
Watch out for
- Requires raw input data to be in Thermo .raw format.
- Requires a strictly formatted reference TSV file containing theoretical retention times and compound m/z values.
- Designed specifically for targeted ribonucleoside quality control rather than general untargeted metabolomics.
Questions
Can I run nf-core/ribomsqc without my own cluster?
The research agent runs nf-core/ribomsqc with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/ribomsqc under?
MIT, like every nf-core pipeline.
What inputs are required to run the pipeline?
A samplesheet CSV file specifying sample identifiers and paths to Thermo .raw files, as well as an analytes TSV file specifying compound names, theoretical retention times, and m/z values.
What software processes the raw spectrometer files?
Raw files are converted with ThermoRawFileParser, and extracted ion chromatograms are extracted using MSnbase.
Can retention time and mass tolerances be customised?
Yes, parameters such as --rt_tolerance (in seconds) and --mz_tolerance can be set at runtime.
How are results visualised?
Processed quality control metrics are merged into JSON files and compiled into an interactive MultiQC report.
How to cite it
Ewels PA et al. (2020) The nf-core framework. Nat Biotechnol. doi:10.1038/s41587-020-0439-x
Written from nf-core/ribomsqc's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.