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Deciphering the ovarian cancer ascites fluid peptidome.

Bery A, Leung F, Smith CR, Diamandis EP, Kulasingam V - Clin Proteomics (2014)

Bottom Line: The resultant fractions were analyzed using an Orbitrap mass spectrometer.We identified over 2000 unique endogenous peptides derived from 259 proteins.Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. vathany.kulasingam@uhn.ca.

ABSTRACT

Background: Conventional proteomic approaches have thus far been unable to identify novel serum biomarkers for ovarian cancer that are more sensitive and specific than the current clinically used marker, CA-125. Because endogenous peptides are smaller and may enter the circulation more easily than proteins, a focus on the low-molecular-weight region may reveal novel biomarkers with enhanced sensitivity and specificity. In this study, we deciphered the peptidome of ascites fluid from 3 ovarian cancer patients and 3 benign individuals (ascites fluid from patients with liver cirrhosis).

Results: Following ultrafiltration of the ascites fluids to remove larger proteins, each filtrate was subjected to solid phase extraction and fractionated using strong cation exchange chromatography. The resultant fractions were analyzed using an Orbitrap mass spectrometer. We identified over 2000 unique endogenous peptides derived from 259 proteins. We then catalogued over 777 peptides that were found only in ovarian cancer ascites. Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

Conclusions: Peptidomics may uncover previously undiscovered disease-specific endogenous peptides that warrant further investigation as biomarkers for ovarian cancer.

No MeSH data available.


Related in: MedlinePlus

Biological repeatability at the peptide (A) and protein (B) level across the 3 benign and 3 ovarian cancer (OvCa) ascites samples. Overlap of unique peptides (A) and corresponding parent proteins (B) identified amongst (i) the three benign control ascites samples and (ii) the three OvCa ascites samples. These samples represent biological replicates (not technical replicates). Each sample was analyzed in singleton.
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Figure 3: Biological repeatability at the peptide (A) and protein (B) level across the 3 benign and 3 ovarian cancer (OvCa) ascites samples. Overlap of unique peptides (A) and corresponding parent proteins (B) identified amongst (i) the three benign control ascites samples and (ii) the three OvCa ascites samples. These samples represent biological replicates (not technical replicates). Each sample was analyzed in singleton.

Mentions: FigureĀ 3 (A) and (B) shows the overlap of identified peptides and proteins, respectively, within the group of 3 OvCa samples and the group of 3 benign samples. About 37-39% of peptides and 50-58% of proteins were found in at least 2 samples. These data are to be expected if we consider the biological heterogeneity of these samples (they all came from different individuals).


Deciphering the ovarian cancer ascites fluid peptidome.

Bery A, Leung F, Smith CR, Diamandis EP, Kulasingam V - Clin Proteomics (2014)

Biological repeatability at the peptide (A) and protein (B) level across the 3 benign and 3 ovarian cancer (OvCa) ascites samples. Overlap of unique peptides (A) and corresponding parent proteins (B) identified amongst (i) the three benign control ascites samples and (ii) the three OvCa ascites samples. These samples represent biological replicates (not technical replicates). Each sample was analyzed in singleton.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230032&req=5

Figure 3: Biological repeatability at the peptide (A) and protein (B) level across the 3 benign and 3 ovarian cancer (OvCa) ascites samples. Overlap of unique peptides (A) and corresponding parent proteins (B) identified amongst (i) the three benign control ascites samples and (ii) the three OvCa ascites samples. These samples represent biological replicates (not technical replicates). Each sample was analyzed in singleton.
Mentions: FigureĀ 3 (A) and (B) shows the overlap of identified peptides and proteins, respectively, within the group of 3 OvCa samples and the group of 3 benign samples. About 37-39% of peptides and 50-58% of proteins were found in at least 2 samples. These data are to be expected if we consider the biological heterogeneity of these samples (they all came from different individuals).

Bottom Line: The resultant fractions were analyzed using an Orbitrap mass spectrometer.We identified over 2000 unique endogenous peptides derived from 259 proteins.Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. vathany.kulasingam@uhn.ca.

ABSTRACT

Background: Conventional proteomic approaches have thus far been unable to identify novel serum biomarkers for ovarian cancer that are more sensitive and specific than the current clinically used marker, CA-125. Because endogenous peptides are smaller and may enter the circulation more easily than proteins, a focus on the low-molecular-weight region may reveal novel biomarkers with enhanced sensitivity and specificity. In this study, we deciphered the peptidome of ascites fluid from 3 ovarian cancer patients and 3 benign individuals (ascites fluid from patients with liver cirrhosis).

Results: Following ultrafiltration of the ascites fluids to remove larger proteins, each filtrate was subjected to solid phase extraction and fractionated using strong cation exchange chromatography. The resultant fractions were analyzed using an Orbitrap mass spectrometer. We identified over 2000 unique endogenous peptides derived from 259 proteins. We then catalogued over 777 peptides that were found only in ovarian cancer ascites. Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

Conclusions: Peptidomics may uncover previously undiscovered disease-specific endogenous peptides that warrant further investigation as biomarkers for ovarian cancer.

No MeSH data available.


Related in: MedlinePlus