@article{SchornVerhoevenRidderetal.2021, author = {Schorn, Michelle A. and Verhoeven, Stefan and Ridder, Lars and Huber, Florian and Acharya, Deepa D. and Aksenov, Alexander A. and Aleti, Gajender and Moghaddam, Jamshid Amiri and Aron, Allegra T. and Aziz, Saefuddin and Bauermeister, Anelize and Bauman, Katherine D. and Baunach, Martin and Beemelmanns, Christine and Beman, J. Michael and Berlanga-Clavero, Mar{\´i}a Victoria and Blacutt, Alex A. and Bode, Helge B. and Boullie, Anne and Brejnrod, Asker and Bugni, Tim S. and Calteau, Alexandra and Cao, Liu and Carri{\´o}n, V{\´i}ctor J. and Castelo-Branco, Raquel and Chanana, Shaurya and Chase, Alexander B. and Chevrette, Marc G. and Costa-Lotufo, Leticia V. and Crawford, Jason M. and Currie, Cameron R. and Cuypers, Bart and Dang, Tam and de Rond, Tristan and Demko, Alyssa M. and Dittmann, Elke and Du, Chao and Drozd, Christopher and Dujardin, Jean-Claude and Dutton, Rachel J. and Edlund, Anna and Fewer, David P. and Garg, Neha and Gauglitz, Julia M. and Gentry, Emily C. and Gerwick, Lena and Glukhov, Evgenia and Gross, Harald and Gugger, Muriel and Guill{\´e}n Matus, Dulce G. and Helfrich, Eric J. N. and Hempel, Benjamin-Florian and Hur, Jae-Seoun and Iorio, Marianna and Jensen, Paul R. and Kang, Kyo Bin and Kaysser, Leonard and Kelleher, Neil L. and Kim, Chung Sub and Kim, Ki Hyun and Koester, Irina and K{\"o}nig, Gabriele M. and Leao, Tiago and Lee, Seoung Rak and Lee, Yi-Yuan and Li, Xuanji and Little, Jessica C. and Maloney, Katherine N. and M{\"a}nnle, Daniel and Martin H, Christian and McAvoy, Andrew C. and Metcalf, Willam W. and Mohimani, Hosein and Molina-Santiago, Carlos and Moore, Bradley S. and Mullowney, Michael W. and Muskat, Mitchell and Nothias, Louis-F{\´e}lix and O'Neill, Ellis C. and Parkinson, Elizabeth I. and Petras, Daniel and Piel, J{\"o}rn and Pierce, Emily C. and Pires, Karine and Reher, Raphael and Romero, Diego and Roper, M. Caroline and Rust, Michael and Saad, Hamada and Saenz, Carmen and Sanchez, Laura M. and S{\o}rensen, S{\o}ren Johannes and Sosio, Margherita and S{\"u}ssmuth, Roderich D. and Sweeney, Douglas and Tahlan, Kapil and Thomson, Regan J. and Tobias, Nicholas J. and Trindade-Silva, Amaro E. and van Wezel, Gilles P. and Wang, Mingxun and Weldon, Kelly C. and Zhang, Fan and Ziemert, Nadine and Duncan, Katherine R. and Cr{\"u}semann, Max and Rogers, Simon and Dorrestein, Pieter C. and Medema, Marnix H. and van der Hooft, Justin J. J.}, title = {A community resource for paired genomic and metabolomic data mining}, series = {Nature Chemical Biology}, volume = {17}, journal = {Nature Chemical Biology}, number = {4}, publisher = {Nature}, issn = {1552-4469}, doi = {10.1038/s41589-020-00724-z}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34708}, pages = {363 -- 368}, year = {2021}, language = {en} } @article{BittremieuxSchmidHuberetal.2022, author = {Bittremieux, Wout and Schmid, Robin and Huber, Florian and van der Hooft, Justin J. J. and Wang, Mingxun and Dorrestein, Pieter C.}, title = {Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules}, series = {Journal of the American Society for Mass Spectrometry}, volume = {33}, journal = {Journal of the American Society for Mass Spectrometry}, number = {9}, publisher = {American Chemical Society (ACS)}, issn = {1044-0305}, doi = {10.1021/jasms.2c00153}, pages = {1733 -- 1744}, year = {2022}, language = {en} } @article{BittremieuxLevitskyPilzetal.2023, author = {Bittremieux, Wout and Levitsky, Lev and Pilz, Matteo and Sachsenberg, Timo and Huber, Florian and Wang, Mingxun and Dorrestein, Pieter C.}, title = {Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils}, series = {Journal of proteome research}, volume = {22}, journal = {Journal of proteome research}, number = {2}, publisher = {American Chemical Society (ACS)}, issn = {1535-3893}, doi = {10.1021/acs.jproteome.2c00632}, pages = {625 -- 631}, year = {2023}, language = {en} } @article{deJongeHechtStrobeletal.2024, author = {de Jonge, Niek F. and Hecht, Helge and Strobel, Michael and Wang, Mingxun and van der Hooft, Justin J. J. and Huber, Florian}, title = {Reproducible MS/MS library cleaning pipeline in matchms}, series = {Journal of Cheminformatics}, volume = {16}, journal = {Journal of Cheminformatics}, number = {1}, publisher = {Springer Nature}, issn = {1758-2946}, doi = {10.1186/s13321-024-00878-1}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-46491}, year = {2024}, abstract = {Mass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is the availability of high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility, and reproducibility as leading principles.Scientific contributionThis pipeline will result in cleaner public mass spectral libraries that will improve library searching and the quality of machine-learning training datasets in mass spectrometry. This pipeline builds on previous work by adding new functionality for curating and correcting annotated libraries, by validating structure annotations. Due to the high quality of our software, the reproducibility, and improved logging, we think our new pipeline has the potential to become the standard in the field for cleaning tandem mass spectrometry libraries.}, subject = {Massenspektrometrie}, language = {en} }