title: Integrated SDS removal and protein digestion by hollow fiber membrane based device for SDS-assisted proteome analysis.
abstract: In this work, a novel integrated sample preparation device for SDS-assisted proteome analysis was developed, by which proteins dissolved in 4% (w/v) SDS were first diluted by 50% methanol, and then SDS was online removed by a hollow fiber membrane interface (HFMI) with 50mM ammonium bicarbonate (pH 8.0) as an exchange buffer, finally digested by an immobilized enzyme reactor (IMER). To evaluate the performance of such an integrated device, bovine serum albumin dissolved in 4% (w/v) SDS as a model sample was analyzed; it could be found that similar to that obtained by direct analysis of BSA digests without SDS (the sequence coverage of 60.3±1.0%, n=3), with HFMI as an interface for SDS removal, BSA was identified with the sequence coverage of 61.0±1.0% (n=3). However, without SDS removal by HFMI, BSA could not be digested by the IMER and none peptides could be detected. In addition, such an integrated sample preparation device was also applied for the analysis of SDS extracted proteins from rat brain, compared to those obtained by filter-aided sample preparation (FASP), not only the identified protein group and unique peptide number were increased by 12% and 39% respectively, but also the sample pretreatment time was shortened from 24h to 4h. All these results demonstrated that such an integrated sample preparation device would provide an alternative tool for SDS assisted proteome analysis.
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Science, Beijing 100039, China.
authors.forename: Simin
authors.initials: S
authors.lastname: Xia
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China.
authors.forename: Huiming
authors.initials: H
authors.lastname: Yuan
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Science, Beijing 100039, China.
authors.forename: Yuanbo
authors.initials: Y
authors.lastname: Chen
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Liang
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China. Electronic address: lihuazhang@dicp.ac.cn.
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian 116023, China.
authors.forename: Yukui
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001923:Brain Chemistry; D004800:Enzymes, Immobilized / Q000737:chemistry / Q000378:metabolism; D004867:Equipment Design; D008567:Membranes, Artificial; D009862:Online Systems; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D051381:Rats; D012710:Serum Albumin, Bovine / Q000032:analysis / Q000737:chemistry; D012967:Sodium Dodecyl Sulfate / Q000302:isolation & purification*; D053719:Tandem Mass Spectrometry; D014357:Trypsin / Q000737:chemistry / Q000378:metabolism
chemical_list: D004800:Enzymes, Immobilized; D008567:Membranes, Artificial; D011506:Proteins; D012710:Serum Albumin, Bovine; D012967:Sodium Dodecyl Sulfate; D014357:Trypsin
keywords: Hollow fiber membrane interface; Immobilized enzymatic reactor; On-line digestion; Proteome analysis; SDS removal