Table 1. Drosophila Cardiac Peptidome.

Peptide Class1	Type of Peptide Evidence	# IdentifiedPeptides (%)	New Peptides
Class 1a	identifies one protein - one gene-model	2316 (44.8)	627
Class 1b	identifies one protein - encoded by isoforms differing in 5′ or 3′ UTR of one gene model	783 (15.1)	146
Class 2a	identifies a subset of protein isoforms	249 (4.8)	95
Class 2b	common to all protein isoforms encoded by a gene-model	1623 (31.4%)	377
Class 3a	identifies one protein from multiple gene-models	13 (0.3%)	1
Class 3b	peptides common to unrelated proteins	185 (3.6)	47

¹See Table S14.

Peptides identified in a shotgun proteomics experiment may be classified into 6 types on the basis of the information they impart about a gene model [32]. Proteotypic peptides are those that uniquely identify a specific protein isoform and may be encoded by multiple transcripts or multiple genes. Information-rich peptides are shared among protein isoforms arising from multiple transcripts or genes. Proteotypic peptides are particularly useful for the design of new high-sensitivity quantitative mass spectrometry methods based on multiple-reaction monitoring. New peptides were not previously in the Drosophila peptide compendium of Brunner et al. [24].