An automated plasma protein fractionation design: high-throughput perspectives for proteomic analysis

BMC Research Notes

Table 1 LC-MALDI-TOF-TOF results

Workflow	No. of MS Spectra^a	No. of total MS/MS Spectra	No. of MS/MS Spectra (mean of all LC-run)	Total identified Peptides	Non redundant identified peptides^b	Mean of proteins ± SD (n total protein)^c	MS/MS efficiency (%)^d	Peptides/ Proteins ± SD	Proteins identified by a single peptide (%)
Anionic	125	7100	888	2700	1305	163 ± 87.6 (326)	38%	3.8 ± 4.3	15 (4,6%)
Cationic	125	5832	729	1432	718	94 ± 39.6 (188)	26%	3.9 ± 4.4	11 (1,5%)
Lipophilic	125	6554	819	1480	691	99 ± 5.6 (198)	23%	4.0 ± 4.2	9 (1,3%)

a) number of total MS spectra/workflow; b) Peptide counts are based on non- redundant identifications in technical replicates and/or in redundant acquisitions of the same sample; c) Mean ± SD of identified proteins in four and three technical replicates for SPE-LC-MS/MS analysis and in brackets number of total identified proteins; d) Efficiency is determined dividing the number of identified peptides per MS/MS spectra.

ISSN: 1756-0500