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. Author manuscript; available in PMC: 2019 May 1.
Published in final edited form as: J Am Soc Mass Spectrom. 2018 Mar 19;29(5):935–947. doi: 10.1007/s13361-018-1915-0

Table 1. Peptide Identification Metrics.

Summary of peptide-spectrum-match (PSM), unique peptide, protein, protein group (proteins collapsed into indistinguishable protein identifications), and phosphopeptide identifications in each group of experiments.

Experiment Trypsin PSMs (%FDR) Unique
Peptides (% FDR)		 Unique
Proteins/Groups (% FDR)* 		Unique
Phosphopeptides (% total)
AP − 68114 (0.1) 7361 (0.9) 680/530 (0.9) 264 (3.6)
AP + 47154 (0.1) 5224 (0.9) 905/715 (0.9) 226 (4.3)
IMAC − 404 (0.2) 191 (0.5) 27/18 (0.0) 107 (56.0)
IMAC + 1554 (0.4) 514 (0.9) 21/19 (0.0) 340 (66.1)
*

FDR was calculated at the protein-level