Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns

Table 4 Summary of peptide and protein identification after application of depletion methods and peptides prefractionation.

	Number of spectra identified	Number of unique peptides identified¹	Number of proteins identified²
IgY14_1	893	571	136
IgY14_2	823	473	124
IgY14_3	881	463	120
Total unique		775	156
IgYHSA_1	837	518	105
IgYHSA_2	804	493	112
IgYHSA_3	652	366	84
Total unique		665	131
Undepl_1	724	277	67
Undepl_2	795	355	78
Undepl_3	773	384	75
Total unique		466	90
IgYHSA-RP30_1	15,992	2,470	433
IgYHSA-RP30_2	12,549	2,282	396
IgYHSA-RP30_3	12,381	2,164	390
Total unique		3,026	535

CSF samples were analyzed as triplicates following depletion of 14 proteins (IgY14), albumin only (IgYHSA) or no depletion (Undepl). Additionally CSF samples were analyzed after albumin depletion and further fractionation by reversed-phase liquid chromatography (IgYHSA-RP30).
1. only hits with Peptide Prophet ≥ 0.95
2. protein identification with Peptide Prophet ≥ 0.9.

ISSN: 1559-0275