Introduction

Use nf-core/ribomsqc to:

• Perform automated quality control of ribonucleoside analysis by mass spectrometry.
• Summarize and visualize QC metrics through integrated MultiQC reports.

Figure 1: General workflow overview showing the pipeline steps from RAW file input through ThermoRawFileParser conversion, MSNBase XIC extraction, JSON merging, to final MultiQC report generation.

Figure 2: Detailed workflow diagram illustrating the data flow and process connections in the ribomsqc pipeline.

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.1038/s41587-020-0439-x