Comparison of 1-D and 2-D LC MS/MS methods for proteomic analysis of human serum.
1-D and 2-D LC methods were utilized for proteome analysis of undepleted human serum. Separation of peptides in 2-D LC was performed either with strong cation exchange (SCX)-RP chromatography or with an RP-RP 2-D LC approach. Peptides were identified by MS/MS using a data-independent acquisition approach. A peptide retention prediction model was used to highlight the potential false-positive peptide identifications. When applying selected data filtration, we identified 52 proteins based on 316 peptides in serum in 1-D LC setup. One hundred and eighty-four proteins/1036 peptides and 142 proteins/905 peptides were identified in RP-RP and SCX-RP 2-D LC, respectively. The performance of both 2-D LC methods for proteomic analysis is critically compared.
Gilar
Martin
M
Waters Corporation, Milford, MA 01757, USA. martin_gilar@waters.com
Olivova
Petra
P
Chakraborty
Asish B
AB
Jaworski
Aleksander
A
Geromanos
Scott J
SJ
Gebler
John C
JC
D053801:Capillary Electrochromatography / Q000379:methods; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D002852:Chromatography, Ion Exchange / Q000379:methods; D002853:Chromatography, Liquid / Q000379:methods*; D006801:Humans; D010455:Peptides / Q000097:blood*; D020543:Proteome / Q000032:analysis*; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010455:Peptides; D020543:Proteome