Introduction

pyXLMS is a python package and web application with graphical user interface that aims to simplify and streamline the intermediate step of connecting crosslink search engine results with down-stream analysis tools, enabling researchers even without bioinformatics knowledge to conduct in-depth crosslink analyses and shifting the focus from data transformation to data interpretation and therefore gaining biological insight.

Figure 1: Overview of available functionality in pyXLMS as of version 1.4.3 [August 2025].

Currently pyXLMS supports input from seven different crosslink search engines: MaxLynx (part of MaxQuant) , MeroX , MS Annika , pLink 2 and pLink 3 , Scout , xiSearch  and xiFDR , XlinkX , as well as the mzIdentML format  of the HUPO Proteomics Standards Initiative, and a well-documented and human-readable custom tabular format .

Down-stream analysis is facilitated by functionality that is directly available within pyXLMS such as validation, annotation, aggregation, filtering, and visualization - and much more  - of crosslink-spectrum-matches and crosslinks. In addition, the data can easily be exported to the required data format of the various available down-stream analysis tools such as xiNET , xiVIEW , xiFDR , XlinkDB , xlms-tools , pyMOL (via pyXlinkViewer ), ChimeraX (via XMAS ), or IMP-X-FDR .