Mass spectrometry data format handling

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/mass-spectrometry-data-format-handling

Use when you have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM transition.From its SKILL.md

Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill mass-spectrometry-data-format-handling

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

15 stars15 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its file declares

Copied from the file, not written here

The file declares its own license as CC-BY-4.0. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

6.0 KB, 958 tokens by cl100k_base, as published. Nobody here has run it

mass-spectrometry-data-format-handling

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.

Summary

Extract precursor and product m/z values from LC-MS/MS MRM (multiple reaction monitoring) raw data files using specialized utility software. This skill transforms raw instrument output into structured m/z pair tables, which serve as the foundation for subsequent MRM transition quantification workflows.

When to use

You have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM transition. This is the initial data parsing step when you do not have pre-extracted transition lists and must recover them from the instrument's raw data format.

When NOT to use

Input already contains a pre-extracted or vendor-supplied transition list in tabular form.
Data was acquired using a non-MRM acquisition mode (e.g., full-scan, data-dependent acquisition).
Raw data file format is not natively supported by the get_PrecMZ_ProdMZ utility.

Inputs

raw MRM sample file (LC-MS/MS instrument format)

Outputs

structured table of precursor m/z and product m/z pairs (CSV or TSV format)

How to apply

Install the get_PrecMZ_ProdMZ utility into the MRMQuant v2.7 associated programs folder. Load the raw MRM sample file (native LC-MS/MS instrument format) into the utility, which will parse the file to identify all MRM transitions and their associated precursor and product m/z values. The program extracts and tabulates these m/z pairs and outputs them in a structured table format (CSV or TSV). Verify that every expected transition is present in the output table and that m/z values match the instrument's acquisition method.

Related tools

MRMQuant (parent software package; provides the framework and associated programs folder in which get_PrecMZ_ProdMZ is installed) — https://github.com/kslynn128171/MRMQuant
get_PrecMZ_ProdMZ (utility for extracting precursor and product m/z values from MRM sample files) — https://github.com/kslynn128171/MRMQuant

Evaluation signals

Output table contains one row per MRM transition with distinct precursor m/z and product m/z columns.
All MRM transitions configured in the instrument's acquisition method are represented in the output.
m/z values are numeric, positive, and fall within the expected mass range for the analytes and instrument.
Output file conforms to declared format (CSV or TSV) with proper delimiters and no truncated or malformed entries.
Row count and transition list match the instrument method file or vendor software's transition report.

Limitations

Utility depends on MRMQuant v2.7; compatibility with older or newer versions is not documented.
No changelog or version history provided; breaking changes in file format support are not communicated.
Success depends on the raw data file format being recognized by the underlying parser; unsupported or corrupted files may fail silently or produce incomplete output.

Evidence

[other] The get_PrecMZ_ProdMZ program is an associated utility that reads an MRM sample file and acquires precursor and product m/z values for each transition.: "The get_PrecMZ_ProdMZ program is an associated utility that reads an MRM sample file and acquires precursor and product m/z values for each transition."
[readme] Users can install get_PrecMZ_ProdMZ in the "program/associated programs" folder to acquire precursor and product m/z values in an MRM sample file.: "Users can install get_PrecMZ_ProdMZ in the "program/associated programs" folder to acquire precursor and product m/z values in an MRM sample file."
[other] Parse the file to identify all MRM transitions and their associated precursor m/z and product m/z values. Extract and tabulate precursor and product m/z pairs for each transition. Output the extracted m/z values in a structured table format (CSV or TSV).: "Parse the file to identify all MRM transitions and their associated precursor m/z and product m/z values. Extract and tabulate precursor and product m/z pairs for each transition. Output the"
[readme] Be sure to use the latest version (currently MRMQuant v2.7).: "Be sure to use the latest version (currently MRMQuant v2.7)."

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.