Meet FIORA! An in silico fragmentation algorithm designed to predict tandem mass spectra (MS/MS) with high accuracy. Using graph neural networks, FIORA models bond cleavages, fragment intensities, and estimates retention times (RT) and collision cross sections (CCS).

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 cleavable and non-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.

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

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

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

Generate a spectral library for Spectronaut from MS Annika results.

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