A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples.
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.
Lopez
Mary F
MF
PerkinElmer Life and Analytical Sciences, Wellesley, MA 02481-4008, USA. mary.lopez@perkinelmer.com
Mikulskis
Alvydas
A
Kuzdzal
Scott
S
Golenko
Eva
E
Petricoin
Emanuel F
EF
Liotta
Lance A
LA
Patton
Wayne F
WF
Whiteley
Gordon R
GR
Rosenblatt
Kevin
K
Gurnani
Prem
P
Nandi
Animesh
A
Neill
Samuel
S
Cullen
Stuart
S
O'Gorman
Martin
M
Sarracino
David
D
Lynch
Christopher
C
Johnson
Andrew
A
Mckenzie
William
W
Fishman
David
D
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
D014408:Biomarkers, Tumor; D001798:Blood Proteins; D002352:Carrier Proteins; D010455:Peptides