MassIVE-KB v1 30 million PSMs

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, resulting in 30,504,897 PSMs for 1,601,479 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").