title: Fractionation of complex protein mixture by virtual three-dimensional liquid chromatography based on combined pH and salt steps.
abstract: The complexity and diversity of biological samples in proteomics require intensive fractionation ahead of mass spectrometry identification. This work developed a chromatographic method called virtual three-dimensional chromatography to fractionate complex protein mixtures. By alternate elution with different pHs and salt concentrations, we implemented pH and salt steps by turns on a single strong cation exchange column to fully exploit its chromatographic ability. Given standard proteins that were not resolved solely by pH or salt gradient elution could be successfully separated using this combined mode. With a reversed phase column tandem connected behind, we further fractionated as well as desalted proteins as the third dimension. This present strategy could readily be adapted with respect to special complexity of biological samples. Crude plasma without depleting high abundance proteins were fractionated by this three-dimensional mode and then analyzed by reversed phase liquid chromatography coupled with LTQ mass spectrometry. In total, 1933 protein groups with wide dynamic ranges were identified from a single experiment. Some characteristics that correlated to the behavior of proteins on strong cation exchange columns are also discussed.
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Zhi-Bin
authors.initials: ZB
authors.lastname: Ning
authors.forename: Qing-Run
authors.initials: QR
authors.lastname: Li
authors.forename: Jie
authors.initials: J
authors.lastname: Dai
authors.forename: Rong-Xia
authors.initials: RX
authors.lastname: Li
authors.forename: Chia-Hui
authors.initials: CH
authors.lastname: Shieh
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
mesh_terms: D000818:Animals; D002021:Buffers; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods; D006863:Hydrogen-Ion Concentration; D007526:Isoelectric Point; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods; D010949:Plasma / Q000737:chemistry; D011506:Proteins / Q000032:analysis / Q000302:isolation & purification; D015203:Reproducibility of Results; D012492:Salts / Q000737:chemistry*
chemical_list: D002021:Buffers; D011506:Proteins; D012492:Salts