title: Mass spectrometric characterization of protein structure details refines the proteome signature for invasive ductal breast carcinoma.
abstract: Early diagnosis as well as individualized therapies are necessary to reduce the mortality of breast cancer, and personalized patient care strategies rely on novel prognostic or predictive factors. In this study, with six breast cancer patients, 2D gel analysis was applied for studying protein expression differences in order to distinguish invasive ductal breast carcinoma, the most frequent breast tumor subtype, from control samples. In total, 1203 protein spots were assembled in a 2D reference gel. Differentially abundant spots were subjected to peptide mass fingerprinting for protein identification. Twenty proteins with their corresponding 38 differentially expressed 2D gel spots were contained in our previously reported proteome signature, suggesting that distinct protein forms were contributing. In-depth MS/MS measurements enabled analyses of protein structure details of selected proteins. In protein spots that significantly contributed to our signature, we found that glyceraldehyde-3-phosphate dehydrogenase was N-terminally truncated, pyruvate kinase M2 and nucleoside diphosphate kinase A but not other isoforms of these proteins were of importance, and nucleophosmin phosphorylation at serine residues 106 and 125 were clearly identified. Principle component analysis and hierarchical clustering with normalized quantitative data from the 38 spots resulted in accurate separation of tumor from control samples. Thus, separation of tissue samples as in our initial proteome signature could be confirmed even with a different proteome analysis platform. In addition, detailed protein structure investigations enabled refining our proteome signature for invasive ductal breast carcinoma, opening the way to structure-/function studies with respect to disease processes and/or therapeutic intervention.
authors.affiliation: Proteome Center Rostock, Department for Proteome Research, Institute of Immunology, Medical Faculty, University of Rostock, Schillingallee 69, P.O. Box 100 888, Rostock 18055, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Röwer
authors.forename: Cornelia
authors.initials: C
authors.lastname: Koy
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Toralf
authors.initials: T
authors.lastname: Reimer
authors.forename: Bernd
authors.initials: B
authors.lastname: Gerber
authors.forename: Hans-Jürgen
authors.initials: HJ
authors.lastname: Thiesen
authors.forename: Michael O
authors.initials: MO
authors.lastname: Glocker
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis* / Q000737:chemistry; D015153:Blotting, Western; D001943:Breast Neoplasms / Q000737:chemistry / Q000378:metabolism*; D018270:Carcinoma, Ductal, Breast / Q000737:chemistry / Q000378:metabolism*; D016022:Case-Control Studies; D016000:Cluster Analysis; D015180:Electrophoresis, Gel, Two-Dimensional; D005260:Female; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D009363:Neoplasm Proteins / Q000032:analysis* / Q000737:chemistry; D010449:Peptide Mapping / Q000379:methods; D025341:Principal Component Analysis; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome