Mrm transition extraction

mrm-transition-extraction

Summary

Extract precursor and product m/z value pairs from raw MRM (Multiple Reaction Monitoring) LC-MS/MS sample files using the get_PrecMZ_ProdMZ utility. This skill is essential for downstream MRM quantification workflows that require cataloging all monitored transitions with their exact mass-to-charge ratios.

When to use

Apply this skill when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each transition monitored during data collection. This is a prerequisite step before quantifying peak areas or validating transition specificity in targeted proteomics or metabolomics experiments.

When NOT to use

• Input data is not from an MRM acquisition method (e.g., full-scan MS or data-dependent acquisition) — use full-spectrum extraction instead.
• m/z values and transition definitions are already available in a structured annotation file — skip directly to quantification.
• Using an older version of MRMQuant (< v2.7) where get_PrecMZ_ProdMZ may not be compatible or may not be bundled.

Inputs

• Raw MRM sample file (LC-MS/MS instrument native format)
• MRMQuant v2.7 installation with associated programs folder

Outputs

• Structured table of precursor m/z and product m/z pairs (CSV or TSV format)
• One row per MRM transition with m/z values tabulated

How to apply

Install get_PrecMZ_ProdMZ from the MRMQuant github repository into the program/associated programs folder of MRMQuant v2.7. Load the raw MRM sample file (instrument-native format from the LC-MS/MS instrument) into the utility. The tool parses the file to identify all MRM transitions encoded in the acquisition method, systematically extracting the precursor m/z and product m/z values for each transition pair. The extracted m/z pairs are output in a structured tabular format (CSV or TSV) with one row per transition, enabling validation and downstream use in quantification pipelines.

Related tools

• MRMQuant (Parent quantification framework that provides the associated programs folder and integration environment for get_PrecMZ_ProdMZ) — github.com/kslynn128171/MRMQuant
• get_PrecMZ_ProdMZ (Dedicated utility that reads MRM sample files and extracts precursor and product m/z values for all monitored transitions) — github.com/kslynn128171/MRMQuant

Evaluation signals

• Output table contains one row per unique MRM transition with no duplicates or missing transitions visible in the raw file.
• Precursor m/z and product m/z columns contain numeric values within expected range for the analyte class (e.g., 100–1500 m/z for small molecules, 500–2000 for peptides).
• CSV or TSV output file is well-formed with consistent delimiter use and proper column headers.
• Number of extracted transitions matches the expected count from the instrument's acquisition method or published transition list for the assay.
• m/z values are consistent across multiple replicates of the same sample file (reproducibility check).

Limitations

• The utility depends on correct parsing of instrument-specific raw file formats; compatibility is limited to formats supported by MRMQuant v2.7.
• No changelog is available to track version-specific improvements or bug fixes to the extraction algorithm.
• The tool extracts transitions as defined in the instrument method; it does not validate transition specificity or perform peak-level quality filtering.

Evidence

• [intro] Install get_PrecMZ_ProdMZ step: "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."
• [readme] Version requirement: "Be sure to use the latest version (currently MRMQuant v2.7)."
• [other] Extraction and output methodology: "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)."
• [other] Input file type: "Load the MRM sample file (raw data format from LC-MS/MS instrument)."