RunAssessor: Extracted Proteomics Metadata from mzML Files

RunAssessor is a tool that extracts sample preparation and instrument acquisition parameters from mass spectrometry data files. The dataset includes extracted metadata such as instrument models, isobaric labels, and phosphoenrichment from one complete dataset and test files from 18 other datasets. The metadata is stored in a comprehensive output file and summarized in a standard Sample and Data Relationship Format (SDRF) file.

Use Cases

• Automating metadata annotation for proteomics data reprocessing pipelines based on extracted instrument parameters.
• Validating and supplementing incomplete metadata in public proteomics repositories using the extracted sample preparation details.
• Facilitating the reuse of public proteomics data by generating standard SDRF files from raw mzML files.

Strengths

• Metadata is extracted directly from the raw mass spectrometry data files, potentially improving reliability.
• The tool was demonstrated using one complete dataset and test files from 18 other datasets.
• Output includes a standard Sample and Data Relationship Format (SDRF) file to improve interoperability.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is very small at 22.5 KB, indicating limited scope.

Provenance

Source

figshare, author Marie Andken

Collection Method

Metadata extracted from mzML mass spectrometry files using the RunAssessor tool.

Freshness

Last updated 2026-04-16 11:04:35; freshness should be verified.