Mass Spectrometry Data Format Handling

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)."