MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

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TANDEM: matching proteins with tandem mass spectra

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Activities at the Universal Protein Resource (UniProt)

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A probability-based approach for high-throughput protein phosphorylation analysis and site localization

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Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

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MS-GF+ makes progress towards a universal database search tool for proteomics

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Cardioids reveal self-organizing principles of human cardiogenesis

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The cGAS–STING pathway drives type I IFN immunopathology in COVID-19

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Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression

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Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

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A heterochromatin-dependent transcription machinery drives piRNA expression

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BacPROTACs mediate targeted protein degradation in bacteria

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A human tissue screen identifies a regulator of ER secretion as a brain-size determinant

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Mass Spectrometry-Based Methods for Identifying Oxidized Proteins in Disease: Advances and Challenges

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Inhibition of CBLB protects from lethal Candida albicans sepsis

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Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess

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A conserved fertilization complex bridges sperm and egg in vertebrates

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Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy

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Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids

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Production of Over 27 000 Peptide and Nearly 4400 Protein Identifications by Single-Shot Capillary-Zone Electrophoresis–Mass Spectrometry via Combination of a Very-Low-Electroosmosis Coated Capillary, a Third-Generation Electrokinetically-Pumped Sheath-Flow Nanospray Interface, an Orbitrap Fusion Lumos Tribrid Mass Spectrometer, and an Advanced-Peak-Determination Algorithm

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EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex

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eIF4E1b is a non-canonical eIF4E protecting maternal dormant mRNAs

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Single-Shot Capillary Zone Electrophoresis–Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample

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Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

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Interrogation of RNA-protein interaction dynamics in bacterial growth

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Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Gueto-Tettay, C., Tang, D., Happonen, L., Heusel, M., Khakzad, H., Malmström, J., & Malmström, L. (2023) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010457 · Cited by 12

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex

Birklbauer, M. J., Müller, F., Geetha, S. S., Matzinger, M., Mechtler, K., & Dorfer, V. (2024) · Communications Chemistry · doi:10.1038/s42004-024-01386-x · Cited by 11

Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis

Tikanova, P., Ross, J. J., Hagmüller, A., Pühringer, F., Pliota, P., Krogull, D., Stefania, V., Hunold, M., Koreshova, A., Koller, A., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02894-2 · Cited by 7

Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra

Lapin, J., Nilsson, A., Wilhelm, M., & Käll, L. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00063 · Cited by 4

Interrogation of RNA-protein interaction dynamics in bacterial growth

Monti, M., Herman, R., Davey, K., Dawson, C. S., Ule, J., Thomas, G. H., Willis, A. E., Lilley, K. S., & Villanueva, E. (2023) · doi:10.1101/2023.07.03.547468 · Cited by 4

EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery

Wijeratne, H. R. S., Runnebohm, A. M., Barron, M. P., Hampton, A. J., Li, R., Peck Justice, S. A., Lenceski, S. H., Rooney, J. D., Smith-Kinnaman, W. R., Chang, G. S., et al. (2026) · doi:10.64898/2026.01.26.701775 · Cited by 1