: A Comprehensive View of the Proteome.

We describe a new release of the PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The PeptideAtlas summary web page provides "Build overview", "PTM coverage", "Experiment contribution", and "Data set contribution" information. The protein and peptide information can also be accessed via the Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments that identify each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyze PTM results is provided in the PeptideAtlas of this important pathogen. PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578.