. Author manuscript; available in PMC: 2018 Jul 24.

Published in final edited form as: Nat Protoc. 2017 Jul 27;12(8):1683–1701. doi: 10.1038/nprot.2017.054

TABLE 3.

Number of peptides and proteins quantified in a typical discovery experiment in plasma using this workflow.

	Number of peptides quantified		Number of proteins quantified with two or more peptides
	IgY14 only	IgY14-SuperMix	IgY14 only	IgY14-SuperMix
Deep profiling with iTRAQ 4-plex labeling^a	22,100^b	35,240^b	2,570^b	4,631^b
Deep profiling with TMT 10-plex labeling^a	NA	33,079^c	NA	3,175^c
Single shot analysis with TMT 10-plex labeling^d	4,361	9,811	317	652

Fractionation of labeled peptides into 30 fractions by basic RP before LC–MS/MS analysis.

Average number of peptides and proteins quantified in three iTRAQ experiments in three different patient samples.

Number of peptides and proteins quantified in a single TMT10 experiment.

Direct analysis after labeling (no peptide-level fractionation) by LC–MS/MS using a 50-cm column and a 4.5-h gradient.

Note: Any Supplementary Information and Source Data files are available in the online version of the paper.