Table I. Spectra, peptides, and proteins identified and quantified by searching against IPI mouse database of three independent iTRAQ experiments.
| Total spectra | Identified peptides (confidence = 99%) | Identified peptides (confidence = 99%, contribution = 2) | Proteins before grouping (unused >2.0) | Identified proteins (unused >2.0) | Identified proteins (unused ≥4.0) | Quantified proteins (unused ≥4.0) | Non- redundant proteinsa | Total identified proteinsb | |
|---|---|---|---|---|---|---|---|---|---|
| Sample 1 | 48,270 | 21,757 | 6,580 | 3,561 | 1,291 | 1,008 | 1,005 | 1,008 | 1,756 |
| Sample 2-1 | 45,851 | 26,386 | 7,045 | 4,035 | 1,425 | 1,138 | 1,136 | 1,298 | |
| Sample 2-2 | 46,550 | 27,126 | 6,684 | 3,668 | 1,262 | 1,011 | 1,011 | ||
| Sample 3-1 | 49,276 | 31,115 | 6,967 | 4,037 | 1,390 | 1,054 | 1,052 | 1,470 | |
| Sample 3-2 | 48,937 | 32,063 | 8,629 | 4,898 | 1,673 | 1,323 | 1,322 |
a The number of non-redundant proteins of samples 2 and 3 was derived from combining the spectral data from duplicated analyses.
b The number of proteins derived from merging the identified proteins under identical accession numbers and/or gene symbols in three independent biological samples.