title: A proteomics platform combining depletion, multi-lectin affinity chromatography (M-LAC), and isoelectric focusing to study the breast cancer proteome.
abstract: The discovery of breast cancer associated plasma/serum biomarkers is important for early diagnosis, disease mechanism elucidation, and determination of treatment strategy for the disease. In this study of serum samples, a multidimensional fractionation platform combined with mass spectrometric analysis were used to achieve the identification of medium to lower abundance proteins, as well as to simultaneously detect glycan and abundance changes. Immuno-affinity depletion and multi-lectin chromatography (M-LAC) were integrated into an automated HPLC platform to remove high abundance protein and fractionate glycoproteins. The collected glycoproteomes were then subjected to isoelectric focusing (IEF) separation by a digital ProteomeChip (dPC), followed by in-gel digestion and LC-MS analysis using an Orbitrap mass spectrometer. As a result, the total number of identified proteins increased significantly when the IEF fractionation step was included as part of the platform. Relevant proteins with biological and disease significance were observed and the dynamic range of the serum proteome measurement was extended. In addition, potential glycan changes were indicated by comparing proteins in control and cancer samples in terms of their affinity to the multi-lectin column (M-LAC) and the pI profiles in IEF separation. In conclusion, a proteomics platform including high abundance protein depletion, lectin affinity fractionation, IEF separation, and LC-MS analysis has been applied to discover breast cancer-associated proteins. The following candidates, thrombospondin-1 and 5, alpha-1B-glycoprotein, serum amyloid P-component, and tenascin-X, were selected as promising examples of the use of this platform. They show potential abundance and glycan changes and will be further investigated in future studies.
authors.affiliation: Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, Massachusetts, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Zeng
authors.forename: Marina
authors.initials: M
authors.lastname: Hincapie
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Pitteri
authors.forename: Samir
authors.initials: S
authors.lastname: Hanash
authors.forename: Joost
authors.initials: J
authors.lastname: Schalkwijk
authors.forename: Jason M
authors.initials: JM
authors.lastname: Hogan
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
mesh_terms: D014408:Biomarkers, Tumor / Q000097:blood; D001943:Breast Neoplasms / Q000378:metabolism*; D064236:Cartilage Oligomeric Matrix Protein; D002846:Chromatography, Affinity / Q000379:methods*; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D016326:Extracellular Matrix Proteins / Q000097:blood; D005260:Female; D006023:Glycoproteins / Q000097:blood; D006801:Humans; D007525:Isoelectric Focusing / Q000379:methods*; D037102:Lectins / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods; D064235:Matrilin Proteins; D020543:Proteome / Q000032:analysis*; D000683:Serum Amyloid P-Component / Q000032:analysis; D019063:Tenascin / Q000097:blood; D019700:Thrombospondin 1 / Q000097:blood
chemical_list: D014408:Biomarkers, Tumor; D064236:Cartilage Oligomeric Matrix Protein; D016326:Extracellular Matrix Proteins; D006023:Glycoproteins; D037102:Lectins; D064235:Matrilin Proteins; D020543:Proteome; D000683:Serum Amyloid P-Component; C577553:TSP5 protein, human; D019063:Tenascin; D019700:Thrombospondin 1; C081865:tenascin X