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.