nf-core/ribomsqc is a bioinformatics pipeline that processes RAW files from mass spectrometry instruments, converts them to mzML format, extracts XICs for selected analytes, generates plots, and summarizes outputs via MultiQC. It is tailored for quality control of ribonucleoside analysis.
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.
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Prepare a samplesheet with your input data, for example:
id,raw_file Day_5,path/to/Day_5.raw
For more information, see the usage docs on required samplesheet.csv columns.
- Prepare an analytes TSV file (e.g.
qcn1.tsv) with your compounds and theoretical retention times. The TSV must have exactly these columns and format:
short_name long_name mz_M0 mz_M1 mz_M2 ms2_mz rt_teoretical
C Cytidine 50 μg/mL 244.0928 112.0505 555
U Uridine 25 μg/mL 245.0768 113.0346 1566
m3C 3-Methylcytidine methosulfate 100 μg/mL 258.1084 126.0662 508
m5C 5-Methylcytidine 100 μg/mL 258.1084 126.0662 655
Cm 2-O-Methylcytidine 20 μg/mL 258.1084 112.0505 883
m5U 5-Methyluridine 50 μg/mL 259.0925 127.0502 1866
I Inosine 25 μg/mL 269.088 137.0458 1741
m1A 1-Methyladenosine 25 μg/mL 282.1197 150.0774 523
G Guanosine 25 μg/mL 284.0989 152.0567 1726
m7G 7-Methylguanosine 25 μg/mL 298.1146 166.0723 554Note
Replace only the values in the rt_teoretical column with your own retention times (in seconds) for each compound.
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Run the pipeline:
nextflow run nf-core/ribomsqc \ --input samplesheet.csv \ --analytes_tsv qcn1.tsv \ --analyte all \ --rt_tolerance 120 \ --mz_tolerance 7 \ --ms_level 1 \ --outdir results \ -profile singularity
Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option.
For more information, see the usage docs and parameters.
See results page for example output and output docs.
nf-core/ribomsqc was originally written by Roger Olivella.
For help, visit Slack #ribomsqc or see contributing guide.
See CITATIONS.md for tool references.
Ewels PA et al. (2020) The nf-core framework. Nat Biotechnol. doi:10.1038/s41587-020-0439-x