Original title: PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS
Authors: Milan Avila Clasen,Max Ruwolt,Louise U. Kurt,Fabio C Gozzo,Shuai Wang,Tao Chen,Paulo C Carvalho,Diogo Borges Lima,Fan Liu
In an article, the authors discuss the need for better data analysis tools in proteome-wide cross-linking mass spectrometry (XL-MS). They emphasize the importance of having ground-truth standards that accurately mimic the biological complexity of proteins. To address this, the authors develop a set of well-controlled XL-MS standards using recombinant proteins mixed systematically for cross-linking.
The authors then introduce Scout, a search engine for XL-MS that utilizes MS-cleavable cross-linkers. They use one of their standard datasets to guide the development of Scout, and then evaluate its performance using independent datasets and previously published data. Their findings show that Scout offers the best combination of speed, sensitivity, and false-discovery rate control compared to other existing XL-MS software.
Overall, this study highlights the importance of using large recombinant standards in supporting the development and evaluation of XL-MS analysis tools.
Original article: https://www.biorxiv.org/content/10.1101/2023.11.30.569448v1