Usage of MS Annika

MS Annika makes use of the workflow interface in Proteome Discoverer, which should be straight-forward to use. Step by step instructions for people unfamiliar with Proteome Discoverer are given in the tutorial. The next sections also give an overview of parameters, results, example workflows and example data. Typically an analysis with MS Annika takes a few minutes for small samples and up to a few hours for larger samples and proteome-wide searches. Please also refer to the specific sections for Astral and timsTOF data if you are analyzing such data.

Parameters & Results

Please refer to the MS Annika User Manual  for a detailed description of all MS Annika parameters as well as descriptions of all result tables. For further down-stream analysis of MS Annika results we recommend taking a look at MS Annika Extensions .

Validation

MS Annika provides basic validation at the crosslink-spectrum-match and peptide pair or residue pair level. However, for more sophisticated validation we recommend using MS Annika in combination with xiFDR (GitHub  / Homepage ). We have shown  that using MS Annika with xiFDR provides better results than MS Annika alone. You can use xiFDR for validation of MS Annika results by exporting your crosslink-spectrum-matches (CSMs) in Proteome Discoverer and uploading them to pyXLMS  ➡️ go to the Export tab ➡️ and under Export Crosslink-Spectrum-Matches select xiFDR. The exported file can then be directly used with xiFDR for validation and aggregation to protein-protein interaction level.