nf-core/ribomsqc

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Introduction

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.

Usage

1. 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.

2. 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	554

3. 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

For more information, see the usage docs and parameters.

Pipeline output

See results page for example output and output docs.

Credits

nf-core/ribomsqc was originally written by Roger Olivella.

Contributions and Support

For help, visit Slack #ribomsqc or see contributing guide.

Citations

See CITATIONS.md for tool references.

Ewels PA et al. (2020) The nf-core framework. Nat Biotechnol. doi:10.1038/s41587-020-0439-x