title: Optimization of protein identification from digests as analyzed by capillary isoelectric focusing-mass spectrometry.
abstract: Capillary isoelectric focusing (CIEF) is a high-resolution separation technique for the analysis of peptides and protein digests. When coupled to ion trap-mass spectrometry (CIEF-MS) the unique separation mechanism is combined with a highly efficient detection system. In an earlier report, we described aspects of separation and interfacing in connection to the analysis of a digest of set of standard proteins. Now, we report on different aspects of the process of protein identification. Sequest software parameters were optimized by using a standard protein digest. These settings were used for the analysis of periplasmic proteins from Escherichia coli. Since in CIEF peptides are focused according to their pI values, the mobilization time of a particular peptide is dependent on its pI value. Based on this relation, the identification of some peptides was facilitated. Furthermore, the Sequest settings that were used could be evaluated. In total, 159 proteins were identified in a single run.
authors.affiliation: Leiden University, Amsterdam Center for Drug Research, Division of Analytical Biosciences, P.O. Box 9502, 2300 RA Leiden, The Netherlands. harriestorms@zonnet.nl
authors.forename: Henricus F
authors.initials: HF
authors.lastname: Storms
authors.forename: Robert
authors.initials: R
authors.lastname: van der Heijden
authors.forename: Ubbo R
authors.initials: UR
authors.lastname: Tjaden
authors.forename: Jan
authors.initials: J
authors.lastname: van der Greef
mesh_terms: D000595:Amino Acid Sequence; D019075:Electrophoresis, Capillary / Q000379:methods*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D007525:Isoelectric Focusing / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D033903:Periplasmic Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D029968:Escherichia coli Proteins; D010455:Peptides; D033903:Periplasmic Proteins