MS Amanda 2.0: Advancements in the standalone implementation

Rationale: Database search engines are the preferred method to identify peptides in mass spectrometry data. However, valuable software is in this context not only defined by a powerful algorithm to separate correct from false identifications, but also by constant maintenance and continuous improvements. Methods: In 2014, we presented our peptide identification algorithm MS Amanda, showing its suitability for identifying peptides in high-resolution tandem mass spectrometry data and its ability to outperform widely used tools to identify peptides. Since then, we have continuously worked on improvements to enhance its usability and to support new trends and developments in this fast-growing field, while keeping the original scoring algorithm to assess the quality of a peptide spectrum match unchanged. Results: We present the outcome of these efforts, MS Amanda 2.0, a faster and more flexible standalone version with the original scoring algorithm. The new implementation has led to a 3–5× speedup, is able to handle new ion types and supports standard data formats. We also show that MS Amanda 2.0 works best when using only the most common ion types in a particular search instead of all possible ion types. Conclusions: MS Amanda is available free of charge from https://ms.imp.ac.at/index.php?action=msamanda.