Software
Here is an overview of the software that we have published:
MS Amanda
MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.
MS Ana
MS Ana is a scoring system to identify peptides in tandem mass spectrometry data using a library of previously identified spectra. Furthermore, MS Ana can create decoy spectral libraries for validation and run searches for additional modifications not found in the spectral library.
MS Annika
MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.
MS Andrea
MS Andrea is an open modification search engine that is designed to directly identify peptide modifications on the PSM level. MS Andrea uses a sequence tag-based approach for filtering peptide candidates before score-based filtering and final scoring using the MS Amanda scoring function.
pyXLMS
pyXLMS is a python package and web application with graphical user interface that aims to simplify and streamline the intermediate step of connecting crosslink search engine results with down-stream analysis tools.
READ
READ is a python-based tool to orchestrate mass spectrometry-based TMTpro-18plex protein quantification for [single cell] DIA and DDA searches with Chimerys, Spectronaut, and DIA-NN.