ARTICLES pubs.acs.org/acschemicalbiology Isotopic Signature Transfer and Mass Pattern Prediction (IsoStamp):

bS Supporting Information Common goals of mass spectrometry (MS)-based proteomicsexperiments are to identify, characterize, and quantify proteins and their posttranslational modifications from biological samples.1 A popular strategy for protein identification is the bottom-up shotgun proteomics approach. In this method, a mixture of proteins is subjected to proteolytic digestion, the resulting peptides are separated by liquid chromatography (LC) and detected by MS, and their parent proteins are inferred from the assigned peptide sequences.2 To convert MS data acquired from proteolytic digests into protein identifications, tandem MS can be used to obtain sequence information for individual peptides, followed by comparison to an in silico proteolytic digest of an organism’s proteome.35 Typically, only the most abun-dant peptides are selected for fragmentation, whereas data for those peptides in relatively low quantities are not obtained.