5 Key Takeaways

• 1

  MassNet standardizes 1.54 billion tandem mass spectra from 648 projects, 27,643 runs, and 35 animal, plant, and microbial species.

• 2

  Reanalysis with FragPipe and Sage yielded 548 million peptide-spectrum matches, 2.54 million unique peptides, and 133,422 proteins.

• 3

  The MSDT format stores spectra with peptide identifications and experimental metadata, and its files were approximately 82% smaller than the source files.

• 4

  Trained on 100 million peptide-spectrum matches, XuanjiNovo outperformed five other de novo sequencing models in a 15-species benchmark.

• 5

  MassNet includes only spectra identified by FragPipe or Sage and does not systematically cover modifications such as phosphorylation, glycosylation, or ubiquitination.