title: Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer.
abstract: BACKGROUND
  Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints) detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry.
  
  
  METHODS
  Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves.
  
  
  RESULTS
  We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions) that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity). Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0.0003) increased level of osteopontin in blood of the group of cancer patients studied (however, the plasma level of osteopontin classified cancer samples with 88% sensitivity but only 28% specificity).
  
  
  CONCLUSIONS
  MALDI-ToF spectrometry of serum has an obvious potential to differentiate samples between early breast cancer patients and healthy controls. Importantly, a classifier built on MS-based serum proteome patterns outperforms available protein biomarkers analyzed in blood by immunoassays.
authors: Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland. m_pietrowska@io.gliwice.pl
authors: Monika
authors: M
authors: Pietrowska
authors: Lukasz
authors: L
authors: Marczak
authors: Joanna
authors: J
authors: Polanska
authors: Katarzyna
authors: K
authors: Behrendt
authors: Elzbieta
authors: E
authors: Nowicka
authors: Anna
authors: A
authors: Walaszczyk
authors: Aleksandra
authors: A
authors: Chmura
authors: Regina
authors: R
authors: Deja
authors: Maciej
authors: M
authors: Stobiecki
authors: Andrzej
authors: A
authors: Polanski
authors: Rafal
authors: R
authors: Tarnawski
authors: Piotr
authors: P
authors: Widlak
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000097:blood*; D001798:Blood Proteins / Q000032:analysis*; D001943:Breast Neoplasms / Q000097:blood* / Q000175:diagnosis* / Q000473:pathology; D016022:Case-Control Studies; D019295:Computational Biology; D005260:Female; D006801:Humans; D007150:Immunohistochemistry; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods; D009367:Neoplasm Staging; D020543:Proteome / Q000032:analysis*; D012680:Sensitivity and Specificity; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D013997:Time Factors
chemical_list: D014408:Biomarkers, Tumor; D001798:Blood Proteins; D020543:Proteome