DescriptionChemical cross-linking in combination with mass spectrometry allows for the identification of amino acid residues in close spatial proximity. These residues can either be on the same protein (intra-link) or on two separate proteins (inter-link). Inter-protein links can be used to identify or to verify protein-protein interactions (PPIs), whereas intra-links can provide spatial restraints for protein structure prediction. Several linkers have been developed over the last years, each with their own physical and chemical properties . The development of MS-cleavable linkers has further boosted the popularity of cross-linking mass spectrometry. These cross-linkers can be fragmented in MS/MS analysis to yield characteristic doublet peaks that correspond to the two cross-linked peptides . Several software packages have been developed for the identification of peptides from spectra containing cross-link information. Most of these tools are designed to identify non-cleavable cross-linkers. Tools aimed at cleavable cross-linkers are often specialised for use with one particular cross-linker, or rely on MS3 data, requiring a specific instrument to measure such data. Since only a fraction of measured spectra contains cross-link information, selection of these spectra is crucial. In addition, these spectra are chimeric spectra and contain fragment ions of both peptides, hampering peptide identification. Here, we present MS Annika, a new cross-linking search engine. The MS Annika algorithm consists of three stages: (1) Cross-link spectra selection based on several different identification modes; (2) Peptide identification using a modified version of the MS Amanda peptide identification algorithm ; and (3) Cross-link validation based on FDR calculation. MS Annika is integrated into Proteome Discoverer 2.3. An exporter utility enables the export of found cross-links to xiView to visualise the results . MS Annika can select cross-link spectra, identify, and verify the contained peptide sequences. MS Annika requires MS2 data only, therefore eliminating the need for MS3 capabilities in mass spectrometers. First results show that the algorithm can compete with comparable tools, such as MeroX  and XLinkX . On a sample data set, MS Annika found 3775 cross-link spectrum matches (CSMs) at 1% FDR. MeroX and XlinkX found 1459 and 3381 at the same false discovery rate, respectively.
|Period||18 Sep 2019|
|Event title||Austrian Proteomics and Metabolomics Research Symposium 2019 (APMRS 2019)|