Spectral libraries

Here you can find the assembled spectral libraries form the current ProteomeTools release.

Spectral libraries (containing raw, unprocessed spectra)

The following libraries are split by fragmentation mode and contain the raw spectrum for best modified peptide, charge combination. The spectra have not undergone peak processing or decharging, but were annotated for their respective sequence. Two versions are available, one including all fragment ions, one containing only annotated fragment ions.The library is available in the NIST .msp text format and are readily usable with Skyline. A generic text format supported by Spectronaut and many other tools will be available soon. For feedback please contact proteometools.proteomics.wzw[at]tum.de

Download current spectra libraries (v_2019-11-12) from ProteomicsDB.org


Spectral library download from external resources

We would like to also point to large public resources which re-processed the data using their pipelines and generated spectral libraries to download. Note that these libraries only contain HCD data and are not split for different collision energies. There might be some non-overlap in peptide numbers.


NIST Peptide Mass Spectral Libraries

The National Institute of Standards and Technology is developing a peptide mass spectral library as an extension of the NIST/EPA/NIH Mass Spectral Library.

Download the human synthetic peptide spectral library.


MassIVE-KB Peptide Spectral Libraries

The Mass Spectrometry Interactive Virtual Environment has reprocessed the synthetic peptide pools in the context of their MassIVE-KB Peptide Spectral Libraries.

Download the ProteomeTools HCD Spectral Library.