Guidelines for reporting quantitative mass spectrometry based experiments in proteomics

Area of Science:

• Proteomics
• Mass Spectrometry
• Data Standardization

Background:

• Mass spectrometry is a key tool for protein identification and quantitative proteomics.
• Methodological advancements enable large-scale protein abundance measurements.
• Various quantitative strategies exist, each with unique data analysis needs.

Purpose of the Study:

• To introduce the MIAPE Quant guidelines for reporting quantitative mass spectrometry data.
• To standardize data handling, representation, and sharing in proteomics.
• To facilitate critical analysis and reproducibility of quantitative proteomics experiments.

Main Methods:

• Development of Minimum Information About a Proteomics Experiment (MIAPE) Quant guidelines by the HUPO Proteomics Standards Initiative (HUPO-PSI).
• Creation of the mzQuantML data exchange format.
• Inclusion of labeled, label-free, and targeted approaches like Selected Reaction Monitoring (SRM).

Main Results:

• The MIAPE Quant guidelines define essential data and metadata for quantitative proteomics.
• These guidelines support data submission to databases and journals.
• The guidelines aim for broad adoption by journals and public proteomics databases.

Conclusions:

• The MIAPE Quant guidelines represent a consensus view for reporting quantitative proteomics data.
• Standardization through these guidelines will improve data quality and reproducibility.
• Adoption is expected to impact proteomics laboratories globally, enhancing data sharing and analysis.