Fiora is an in silico fragmentation algorithm for small compounds that produces simulated tandem mass spectra (MS/MS). The framework employs a graph neural network to predict bond cleavages and fragment ion intensities via edge prediction. Additionally, Fiora can estimate retention times (RT) and collision cross sections (CCS) of the compounds.

Mistle is a fast spectral search engine. It uses a fragment-indexing technique and SIMD intrinsics to match experimental MS2 spectra to large spectral libraries at a high performance.

MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of MS2-cleavable crosslinkers from MS2 and MS3 spectra.

Export MS Annika crosslink results to different formats.

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.

Extensions for better usability of the cross-linking tool MaXLinker.

Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.

Generate a spectral library for Spectronaut from MS Annika results.

A script to merge and optionally validate several MS Annika search results.

List of all available extensions for our cross-linking search engine MS Annika.

Results and Evaluation of the MS3 Search Algorithm of MS Annika.

Extensions to use the cross-linking tool Scout with other software.

A script and functions to group and validate MS Annika results.