Table S4.

Identified proteins and PCs in each Tara Oceans sample using three analytical search pipelines to map peptides detected by all sample preparation methods and mass spectrometers against sequences from paired viral metagenomes to generate the Inclusive Dataset

Sample	SEQUEST with DTASelect			Proteome Discoverer with Percolator			TPP with X! Tandem			All search algorithms
	Total proteins	Unique proteins*	PCs†	Total proteins	Unique proteins*	PCs†	Total proteins	Unique proteins*	PCs†	Total proteins	Unique proteins*	PCs†
22SUR	256	89	100	110	71	49	266	182	132	446	223	195
39SUR	353	278	126	221	171	123	193	156	99	519	278	212
39DCM	236	120	84	336	293	173	293	285	141	527	428	240
67SUR	223	113	85	150	118	96	236	202	141	383	254	181
All samples	1,068	445	281	817	653	299	988	825	377	1,875	1,183	574

^*Proteins that had at least one unique spectra.

^†The number of PCs identified within nonredundant proteins.