MassIVE-KB v1 30 million PSMs training/validation/test splits

The MassIVE-KB data are derived from PSMs used to compile the MassIVE-KB v1 spectral library and consists of approximately 30 million PSMs. The PSMs were obtained by collecting up to the top 100 PSMs for each of the 2,154,269 precursors (as defined by a peptidoform and charge) included in the MassIVE-KB v1 spectral library.

The data are split into peptide-disjoint training, validation, and test sets, consisting of:

• Training: 28,508,636 PSMs for 1,496,701 unique peptidoforms.
• Validation: 1,000,234 PSMs for 52,379 unique peptidoforms.
• Test: 996,027 PSMs for 52,399 unique peptidoforms.

The dataset was originally compiled through the following steps:

• On the MassIVE website, go to MassIVE Knowledge Base > Human HCD Spectral Library > All Candidate library spectra > Download.
• This will give you a zipped TSV file with the metadata and peptide identifications for all 30 million PSMs.
• Using the filename (column "filename") you can then retrieve the corresponding peak files from the MassIVE FTP server (done using a wget script) and extract the desired spectra using their scan number (column "scan").