HolobiomicsLab precursor-product-mz-parsing
Summary
Extract precursor and product m/z value pairs from MRM (multiple reaction monitoring) LC-MS/MS raw data files using the get_PrecMZ_ProdMZ utility. This skill enables automated identification and tabulation of all MRM transitions' mass-to-charge ratios, essential for method validation and quantitation workflow setup.
When to use
Apply this skill when you have raw MRM sample files from a LC-MS/MS instrument and need to systematically recover all precursor m/z and product m/z pairs for each transition. Use this as an initial parsing step before quantitation, method optimization, or transition verification workflows.
When NOT to use
- Input is already a parsed or pre-extracted m/z transition table.
- Working with non-MRM data (e.g., full-scan MS, data-independent acquisition, or other MS/MS acquisition modes).
- Using MRMQuant versions older than v2.7.
Inputs
- Raw MRM sample file (LC-MS/MS instrument format)
Outputs
- Structured table of precursor m/z and product m/z value pairs (CSV or TSV format)
- Tabulated list of all MRM transitions with associated m/z values
How to apply
Install get_PrecMZ_ProdMZ into the MRMQuant v2.7 'program/associated programs' folder from the project repository. Load the raw MRM sample file (native LC-MS/MS instrument format) into the utility. The program parses the file to identify all MRM transitions and their associated precursor and product m/z values. Extract and tabulate the precursor–product m/z pairs for each transition, outputting results in a structured table format (CSV or TSV) for downstream analysis or method documentation.
Related tools
- MRMQuant (Parent quantitation package that hosts and manages get_PrecMZ_ProdMZ as an associated utility for MRM data processing) — github.com/kslynn128171/MRMQuant
- get_PrecMZ_ProdMZ (Dedicated utility for parsing raw MRM files and extracting precursor–product m/z transition data) — github.com/kslynn128171/MRMQuant
Evaluation signals
- Output table contains one row per unique MRM transition with no missing or null m/z values.
- All precursor m/z values match the expected monoisotopic mass or expected parent ion m/z for the target compound.
- All product m/z values fall within the expected fragmentation pattern for the given precursor ion (typically < precursor m/z).
- CSV or TSV output is well-formed, parseable, and contains consistent column headers (e.g., 'Transition', 'Precursor_mz', 'Product_mz').
- Number of transitions extracted matches the expected count from the LC-MS/MS acquisition method file.
Limitations
- Requires MRMQuant v2.7 or later; compatibility with older versions not confirmed.
- Only processes raw MRM sample files; cannot work with already-converted or abstracted data formats.
- No changelog provided in the repository documentation, limiting version-to-version change tracking.
- Depends on successful file format recognition; instrument-specific raw formats may require vendor-specific drivers or converters.
Evidence
- [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] 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] Be sure to use the latest version (currently MRMQuant v2.7).: "Be sure to use the latest version (currently MRMQuant v2.7)."
- [other] Output the extracted m/z values in a structured table format (CSV or TSV).: "Output the extracted m/z values in a structured table format (CSV or TSV)."