title: Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT).
abstract: In the past decade, shotgun proteomic analysis has been utilized extensively to answer complex biological questions. New challenges arise in large scale proteomic profiling when dealing with complex biological mixtures such as the mammalian cell lysate. In this study, we explored the approach of protein separation prior to the shotgun multidimensional protein identification technology (MudPIT) analysis. We fractionated the mammalian cancer cell lysate using the PF 2D ProteomeLab system and analyzed the distribution of molecular weight, isoelectric point, and cellular localization of the eluted proteins. As a result, we were able to reduce sample complexity by protein fractionation and increase the possibility of detecting proteins with lower abundance in the complex protein mixture.
authors.affiliation: Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA. emilyc@scripps.edu
authors.forename: Emily I
authors.initials: EI
authors.lastname: Chen
authors.forename: Johannes
authors.initials: J
authors.lastname: Hewel
authors.forename: Brunhilde
authors.initials: B
authors.lastname: Felding-Habermann
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis* / Q000302:isolation & purification; D001943:Breast Neoplasms / Q000737:chemistry* / Q000556:secondary; D002851:Chromatography, High Pressure Liquid; D002852:Chromatography, Ion Exchange; D015180:Electrophoresis, Gel, Two-Dimensional; D005260:Female; D006801:Humans; D007525:Isoelectric Focusing; D009363:Neoplasm Proteins / Q000032:analysis* / Q000302:isolation & purification; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D020539:Sequence Analysis, Protein; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins