Jim Shofstahl

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion.

Lennart Martens, Harald Barsnes, Yasset Perez-Riverol, 2019, Journal of proteome research.

The HUPO-PSI standardized spectral library format

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020 .

mzML—a Community Standard for Mass Spectrometry Data*

Lennart Martens, Henning Hermjakob, Fredrik Levander, 2010, Molecular & Cellular Proteomics.

Universal Spectrum Identifier for mass spectra

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020, Nature Methods.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

Lennart Martens, Fredrik Levander, Matthew Chambers, 2011, Molecular & Cellular Proteomics.

The PSI-MOD community standard for representation of protein modification data

Luisa Montecchi-Palazzi, Pierre-Alain Binz, Ron Beavis, 2008, Nature Biotechnology.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.