PROSPECT PTMs: Rich Labeled Tandem Mass Spectrometry Dataset of Modified Peptides for Machine Learning in Proteomics Wassim Gabriel 1 Omar Shouman 1 Ayla Schroeder 1

Post-Translational Modifications (PTMs) are changes that occur in proteins after synthesis, influencing their structure, function, and cellular behavior. PTMs are essential in cell biology; they regulate protein function and stability, are involved in various cellular processes, and are linked to numerous diseases. A particularly interesting class of PTMs are chemical modifications such as phosphorylation introduced on amino acid side chains because they can drastically alter the physicochemical properties of the peptides once they are present. One or more PTMs can be attached to each amino acid of the peptide sequence. The most commonly applied technique to detect PTMs on proteins is bottom-up Mass Spectrometrybased proteomics (MS), where proteins are digested into peptides and subsequently analyzed using Tandem Mass Spectrometry (MS/MS).