Exploring the Alternative Proteome with OpenProt and Mass Spectrometry.- Identification of Novel Bacterial Microproteins Encoded by Small Open Reading Frames Using a Computational Proteogenomics Workflow.- Demystifying PTM Identification Using MODplus: Best Practices and Pitfalls.- Understanding PTM Cross-Talk Through a Visualization Tool, PTMViz.- Integrating HexNAcQuest with Glycoproteomics Data Analysis Software to Distinguish HexNAc Isomers on Peptides.- UniCarb-DB, an MS/MS Experimental Glycomic Fragmentation Database.- Integration of Web-Based Tools to Visualize, Integrate, and Interpret Glycogene Expression and Glycomics Data.- PGFinder, an Open Source Software for Peptidoglycomics: The Structural Analysis of Bacterial Peptidoglycan by LC-MS.- Making MS Omics Data ML Ready: SpeCollate Protocols.- AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.- Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.- Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline & ChannelsDB 2.0.- AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses.- Detection and Analysis of Short Linear Motif-Based Protein-Protein Interactions with SLiMAn2 Web Server.- Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods.- SACCHARIS v2: Streamlining Prediction of Carbohydrate-Active Enzyme Specificities Within Large Datasets.- SignalP: The Evolution of a Web Server.
