title: A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples.
abstract: BACKGROUND
  Most cases of ovarian cancer are detected at later stages when the 5-year survival is approximately 15%, but 5-year survival approaches 90% when the cancer is detected early (stage I). To use mass spectrometry (MS) of serum proteins for early detection, a seamless workflow is needed that provides an opportunity for rapid profiling along with direct identification of the underpinning ions.
  
  
  METHODS
  We used carrier protein-bound affinity enrichment of serum samples directly coupled with MALDI orthagonal TOF MS profiling to rapidly search for potential ion signatures that contained discriminatory power. These ions were subsequently directly subjected to tandem MS for sequence identification.
  
  
  RESULTS
  We discovered several biomarker panels that enabled differentiation of stage I ovarian cancer from unaffected (age-matched) patients with no evidence of ovarian cancer, with positive results in >93% of samples from patients with disease-negative results and in 97% of disease-free controls. The carrier protein-based approach identified additional protein fragments, many from low-abundance proteins or proteins not previously seen in serum.
  
  
  CONCLUSIONS
  This workflow system using a highly reproducible, high-resolution MALDI-TOF platform enables rapid enrichment and profiling of large numbers of clinical samples for discovery of ion signatures and integration of direct sequencing and identification of the ions without need for additional offline, time-consuming purification strategies.
authors.affiliation: PerkinElmer Life and Analytical Sciences, Wellesley, MA 02481-4008, USA. mary.lopez@perkinelmer.com
authors.forename: Mary F
authors.initials: MF
authors.lastname: Lopez
authors.forename: Alvydas
authors.initials: A
authors.lastname: Mikulskis
authors.forename: Scott
authors.initials: S
authors.lastname: Kuzdzal
authors.forename: Eva
authors.initials: E
authors.lastname: Golenko
authors.forename: Emanuel F
authors.initials: EF
authors.lastname: Petricoin
authors.forename: Lance A
authors.initials: LA
authors.lastname: Liotta
authors.forename: Wayne F
authors.initials: WF
authors.lastname: Patton
authors.forename: Gordon R
authors.initials: GR
authors.lastname: Whiteley
authors.forename: Kevin
authors.initials: K
authors.lastname: Rosenblatt
authors.forename: Prem
authors.initials: P
authors.lastname: Gurnani
authors.forename: Animesh
authors.initials: A
authors.lastname: Nandi
authors.forename: Samuel
authors.initials: S
authors.lastname: Neill
authors.forename: Stuart
authors.initials: S
authors.lastname: Cullen
authors.forename: Martin
authors.initials: M
authors.lastname: O'Gorman
authors.forename: David
authors.initials: D
authors.lastname: Sarracino
authors.forename: Christopher
authors.initials: C
authors.lastname: Lynch
authors.forename: Andrew
authors.initials: A
authors.lastname: Johnson
authors.forename: William
authors.initials: W
authors.lastname: Mckenzie
authors.forename: David
authors.initials: D
authors.lastname: Fishman
mesh_terms: D014408:Biomarkers, Tumor / Q000097:blood; D001798:Blood Proteins / Q000378:metabolism*; D002352:Carrier Proteins / Q000097:blood*; D005260:Female; D006801:Humans; D010051:Ovarian Neoplasms / Q000097:blood / Q000175:diagnosis*; D010455:Peptides / Q000097:blood*; D011485:Protein Binding; D040901:Proteomics; D012680:Sensitivity and Specificity; D044967:Serum; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D014408:Biomarkers, Tumor; D001798:Blood Proteins; D002352:Carrier Proteins; D010455:Peptides