OpenMS WebApps: Building User-Friendly Solutions for MS Analysis
Journal of Proteome Research2025
Müller, Tom David; Siraj, Arslan; Walter, Axel; Kim, Jihyung; Wein, Samuel; von Kleist, Johannes; Feroz, Ayesha; Pilz, Matteo; Jeong, Kyowon; Sing, Justin Cyril
+ pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas
Journal of Proteome Research2025
Sing, Justin Cyril; Charkow, Joshua; Walter, Axel; Gao, Mingxuan; Muller, Tom David; Bittremieux, Wout; Sachsenberg, Timo; Röst, Hannes Luc
+ A universal language for finding mass spectrometry data patterns
Nature methods2025
Damiani T, Jarmusch AK, Aron AT, Petras D, Phelan VV, Zhao HN, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Fahy E, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kessler N, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto Knaan T, Mannochio-Russo H, Marty MT, Matsuzawa Y, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Neuweger H, Niedermeyer THJ, Nishida K, Northen TR, Overdahl KE, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Subramaniam S, Tian Z, Tripathi A, Tsugawa H, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Pluskal T, Dorrestein PC, Wang M
+ Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata
Journal of proteomics2025
Zheng P, Audain E, Webel H, Dai C, Klein J, Hitz MP, Sachsenberg T, Bai M, Perez-Riverol Y
+ MHCquant2 refines immunopeptidomics tumor antigen discovery
Genome biology2025
Scheid J, Lemke S, Hoenisch-Gravel N, Dengler A, Sachsenberg T, Declerq A, Gabriels R, Bauer J, Wacker M, Bichmann L, Martens L, Dubbelaar ML, Nahnsen S, Walz JS
+ Open-Source and FAIR Research Software for Proteomics
Journal of proteome research2025
Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE
+ Perspectives in computational mass spectrometry: recent developments and key challenges
Bioinformatics advances2025
Sachsenberg T, Pino LK, Brunet M, Bludau I, Kohlbacher O, Vizcaino JA, Bittremieux W
+ mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
Journal of proteome research2025
Van Den Bossche T, Alexandrov T, Bilbao A, Bittremieux W, Brigante FI, Chambers MC, Charkow J, Deutsch E, Dowsey AW, El Abiead Y, Gabriels R, Hecht H, Heuckeroth S, Klein JA, Knierman M, Martens L, Moritz RL, McCall LI, Neumann S, Perez-Riverol Y, Röst HL, Price EJ, Shofstahl J, Tabb DL, Uszkoreit J, Vizcaíno JA, Wang M, Willems S, Winkelhardt D, Kohlbacher O, Wein SP
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