Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data

Table 2 Comparison of the number of peptides identified by different approaches across the eight human gut metaproteomic datasets

	HM403	HM415	HM454	HM455	HM466	HM467	HM494	HM503
	(57,835 ^#)	(59,839)	(53,937)	(64,255)	(60,800)	(58,500)	(58,109)	(59,892)
HAPiID-MSGF	12,962	12,535	17,619	20,803	13,862	15,924	21,108	24,962
HAPiID-X!	12,414	12,180	17,314	21,145	13,676	16,334	21,042	24,459
MetaPro-IQ	12,606	11,562	15,446	17,868	11,302	12,380	18,562	21,879
Matched	13,156*	12,179	15,863	18,677	11,733	12,724	19,248	23,632

^#:Numbers in parentheses indicate the total number of spectra present in each sample. *: The highest numbers of peptides identified in each sample are highlighted in bold; HAPiID-MSGF (HAPiID using MS-GF+ as the search engine); HAPiID-X! (HAPiID using X! Tandem as the search engine); Matched: peptide identification using matched metagenome as the reference. Results for the MetaPro-IQ and matched metagenome approach were taken from [32].

ISSN: 2049-2618