File Format Validation Proteomics

file-format-validation-proteomics

Summary

Validate raw mass spectrometry file formats (.raw, .mzML, .mzXML) and enforce size/integrity constraints before ingestion into the MSConnect platform. This skill ensures only compatible, uncorrupted files enter the data processing pipeline.

When to use

When raw MS files are uploaded to MSConnect via the Raw File Uploader and must be verified for compatibility with downstream processing tools (e.g., Proteomics_Data_Processor) before routing to the processing queue. Apply this skill immediately after file upload but before invoking third-party processors.

When NOT to use

• Input is already a processed feature table or quantification matrix (validation applies only to raw MS files)
• Files have already been validated and stored in a designated repository with integrity guarantees
• The processor tool accepts vendor-specific proprietary formats not covered by the whitelist (consult processor documentation first)

Inputs

• Raw MS file (e.g., .raw, .mzML, .mzXML format)
• File metadata (filename, upload path, file size)
• Processor tool specifications (supported formats, size limits)

Outputs

• Validation status (success, failure, or pending)
• Validation log entry (format, size, integrity check results)
• File metadata tag linking to original upload session (if valid)

How to apply

Implement file validation logic that checks (1) file extension against the whitelist of supported MS raw formats (.raw, .mzML, .mzXML); (2) file size against platform constraints; and (3) file integrity by reading headers or checksums to confirm the file is not corrupted. Log all validation outcomes (success/failure/pending) and reject files that fail any check, returning detailed error messages to the user. This validation gates entry into the Proteomics_Data_Processor tool, preventing malformed or incompatible files from consuming processing resources.

Related tools

• Raw_File_Uploader (Accepts and stages raw MS files for validation via HTTP/HTML form interface) — https://github.com/RTKlab-BYU/Raw_File_Uploader
• Proteomics_Data_Processor (Downstream consumer of validated raw files; requires format compatibility verification before invocation) — https://github.com/RTKlab-BYU/Proteomics_Data_Processor
• MSConnect (Platform orchestrator that routes validated files to the processing queue and logs ingestion outcomes) — https://github.com/RTKlab-BYU/MSConnect

Evaluation signals

• All uploaded .raw, .mzML, .mzXML files are accepted; all files with incorrect extensions are rejected with error message
• File size violations (e.g., exceeding platform limits) are caught and logged before file storage
• Corrupted or truncated files are detected and rejected; valid files are confirmed readable by header inspection or checksum verification
• Validation status (success/failure/pending) is recorded in upload logs and linked to the original user session and project metadata
• Only validated files are passed to Proteomics_Data_Processor; no unvalidated files enter the processing queue

Limitations

• Validation logic must be updated if processor tool specifications change (e.g., new supported formats or size constraints); no automatic discovery of processor requirements
• File integrity checks (checksums, header parsing) may fail for partially uploaded or network-interrupted transfers; retry/resume logic is not covered by this skill alone
• Vendor-specific metadata embedded in .raw files (e.g., Thermo Orbitrap-specific fields) is not validated; only format and size are checked
• No validation of scientific metadata (e.g., sample description, instrument configuration) embedded in file headers; only structural validity is confirmed

Evidence

• [other] Implement file validation logic to verify raw MS file formats (e.g., .raw, .mzML, .mzXML) and enforce size/integrity constraints.: "Implement file validation logic to verify raw MS file formats (e.g., .raw, .mzML, .mzXML) and enforce size/integrity constraints."
• [other] Validate raw file integrity and format compatibility with the Proteomics_Data_Processor tool specifications.: "Validate raw file integrity and format compatibility with the Proteomics_Data_Processor tool specifications."
• [other] Integrate upload status tracking (success/failure/pending) and logging to report ingestion outcomes.: "Integrate upload status tracking (success/failure/pending) and logging to report ingestion outcomes."
• [readme] MSConnect streamlines the entire process from data collection, data management, data processing and to data visualization by integrating and supporting various third-party tools: "MSConnect streamlines the entire process from data collection, data management, data processing and to data visualization by integrating and supporting various third-party tools"
• [readme] The platform is built with Python, Django, JavaScript, and HTML and works with Raw file uploader and Processor: "The platform is built with Python, Django, JavaScript, and HTML and works with Raw file uploader and Processor"