title: Large-scale muLC-MS/MS for silver- and Coomassie blue-stained polyacrylamide gels.
abstract: 2-DE combined with LC-MS/MS has become a routine, reliable protein separation and identification technology for proteome analysis. The demand for large-scale protein identifications after 2-DE separation requires a sensitive and high-throughput LC-MS/MS method. In this report, a simple, splitless, fully automated capillary LC-MS/MS system was described for the large-scale identification of proteins from gels stained with either silver or CBB. The gel samples were digested and peptides were extracted using an in-gel digestion workstation. The peptides were automatically introduced into a capillary column by an autosampler connected to an HPLC pump. A nanoLC pump was then used to deliver the gradient and elute the peptides from the capillary column directly into an LCQ IT mass spectrometer. Neither a peptide trapping setting nor a flow split is needed in this simple setup. The collected MS/MS spectra were then automatically searched by SEQUEST, and filtered and organized by DTASelect. Hundreds of silver-stained or CBB-stained Shewanella oneidensis, Geobacter sulfurreducens, and Geobacter metallireducens proteins separated by denaturing or nondenaturing 2-DE were digested and routinely analyzed using this fully automated muLC-MS/MS system. High peptide hits and sequence coverage were achieved for most CBB-stained gel spots. About 75% of the spots were found to contain multiple proteins. Although silver staining is not commonly thought to be optimal for MS analysis, protein identifications were successfully obtained from silver-stained 2-DE spots detected using methods with and without formaldehyde for protein fixation.
authors.affiliation: Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Wenhong
authors.initials: W
authors.lastname: Zhu
authors.forename: John
authors.initials: J
authors.lastname: Venable
authors.forename: Carol S
authors.initials: CS
authors.lastname: Giometti
authors.forename: Tripti
authors.initials: T
authors.lastname: Khare
authors.forename: Sandra
authors.initials: S
authors.lastname: Tollaksen
authors.forename: Angela J
authors.initials: AJ
authors.lastname: Ahrendt
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D000180:Acrylic Resins / Q000737:chemistry*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000032:analysis*; D002853:Chromatography, Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D045302:Geobacter / Q000378:metabolism; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis; D012394:Rosaniline Dyes / Q000737:chemistry*; D020592:Shewanella / Q000378:metabolism; D016622:Silver Staining
chemical_list: D000180:Acrylic Resins; D001426:Bacterial Proteins; D010455:Peptides; D012394:Rosaniline Dyes; C016680:polyacrylamide gels; C048139:Coomassie blue