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Key Features

Data Conversion

Data Conversion Flow

Convert data from leading proteomics software to standardized QPX format:

  1. MaxQuant result files:

  2. msms.txt: MS/MS scan information (PSM data)

  3. evidence.txt: Peptide evidence (Feature data)
  4. proteinGroups.txt: Protein identification results

  5. *.sdrf.tsv: SDRF-Proteomics metadata (optional)

  6. DIA-NN result files:

  7. report.tsv or report.parquet: DIA-NN main report

  8. pg_matrix.tsv: Protein group matrix
  9. *.sdrf.tsv: SDRF-Proteomics metadata (optional)

  10. *ms_info.parquet: mzML statistics folder (optional)

  11. FragPipe result files:

  12. psm.tsv: PSM identifications

  13. *.sdrf.tsv: SDRF-Proteomics metadata (optional)

  14. OpenMS/idXML files:

  15. *.idXML: Identification results

  16. *.mzML: Corresponding spectra files (optional, for batch processing)

  17. mzTab (quantms pipeline) files:

  18. *.mzTab: Standard proteomics format (PSM/PEP/PRT sections)

  19. *msstats*.csv: MSstats/MSstatsTMT input files (optional)

Output format: All conversions produce standardized parquet files:

  • PSM: *-psm.parquet
  • Feature: *-feature.parquet
  • Protein Group: *-pg.parquet

View all converters →

Data Transformation

Transform and enrich your data:

  • Absolute Expression (AE): iBAQ-based absolute quantification
  • Differential Expression (DE): MSstats statistical analysis
  • Gene Mapping: Add gene annotations
  • UniProt Integration: Latest protein annotations
  • AnnData Export: Integration with single-cell tools

View all transformations →

Visualization

Generate publication-quality plots:

  • Intensity distributions (KDE, box plots)
  • Peptide distribution analysis
  • iBAQ distribution plots
  • Quality control visualizations

View visualization tools →

Statistical Analysis

Comprehensive data statistics:

  • PSM data statistics (proteins, peptides, PSMs count)
  • Project-level absolute expression statistics
  • Sample-level quantitative metrics
  • Automated report generation

View statistical tools →

Project Management

Track and share your work:

  • PRIDE Archive integration
  • Project metadata management
  • File registration and tracking

View project tools →