Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma.

Ju Yeon Lee, Jin Young Kim, Gun Wook Park, Mi Hee Cheon, Kyung Hoon Kwon, Yeong Hee Ahn, Myeong Hee Moon, Hyoung Joo Lee, Young Ki Paik, Jong Shin Yoo

Research output: Contribution to journalArticle

Abstract

A simple mass spectrometric approach for the discovery and validation of biomarkers in human plasma was developed by targeting nonglycosylated tryptic peptides adjacent to glycosylation sites in an N-linked glycoprotein, one of the most important biomarkers for early detection, prognoses, and disease therapies. The discovery and validation of novel biomarkers requires complex sample pretreatment steps, such as depletion of highly abundant proteins, enrichment of desired proteins, or the development of new antibodies. The current study exploited the steric hindrance of glycan units in N-linked glycoproteins, which significantly affects the efficiency of proteolytic digestion if an enzymatically active amino acid is adjacent to the N-linked glycosylation site. Proteolytic digestion then results in quantitatively different peptide products in accordance with the degree of glycosylation. The effect of glycan steric hindrance on tryptic digestion was first demonstrated using alpha-1-acid glycoprotein (AGP) as a model compound versus deglycosylated alpha-1-acid glycoprotein. Second, nonglycosylated tryptic peptide biomarkers, which generally show much higher sensitivity in mass spectrometric analyses than their glycosylated counterparts, were quantified in human hepatocellular carcinoma plasma using a label-free method with no need for N-linked glycoprotein enrichment. Finally, the method was validated using a multiple reaction monitoring analysis, demonstrating that the newly discovered nonglycosylated tryptic peptide targets were present at different levels in normal and hepatocellular carcinoma plasmas. The area under the receiver operating characteristic curve generated through analyses of nonglycosylated tryptic peptide from vitronectin precursor protein was 0.978, the highest observed in a group of patients with hepatocellular carcinoma. This work provides a targeted means of discovering and validating nonglycosylated tryptic peptides as biomarkers in human plasma, without the need for complex enrichment processes or expensive antibody preparations.

Original languageEnglish
JournalMolecular & cellular proteomics : MCP
Volume10
Issue number12
Publication statusPublished - 2011 Dec 1

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Plasma (human)
Biomarkers
Glycoproteins
Glycosylation
Peptides
Orosomucoid
Digestion
Hepatocellular Carcinoma
Polysaccharides
Vitronectin
Plasmas
Protein Precursors
Antibodies
ROC Curve
Labels
Early Diagnosis
Proteins
Amino Acids
Monitoring

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

Cite this

Lee, Ju Yeon ; Kim, Jin Young ; Park, Gun Wook ; Cheon, Mi Hee ; Kwon, Kyung Hoon ; Ahn, Yeong Hee ; Moon, Myeong Hee ; Lee, Hyoung Joo ; Paik, Young Ki ; Yoo, Jong Shin. / Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. In: Molecular & cellular proteomics : MCP. 2011 ; Vol. 10, No. 12.
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abstract = "A simple mass spectrometric approach for the discovery and validation of biomarkers in human plasma was developed by targeting nonglycosylated tryptic peptides adjacent to glycosylation sites in an N-linked glycoprotein, one of the most important biomarkers for early detection, prognoses, and disease therapies. The discovery and validation of novel biomarkers requires complex sample pretreatment steps, such as depletion of highly abundant proteins, enrichment of desired proteins, or the development of new antibodies. The current study exploited the steric hindrance of glycan units in N-linked glycoproteins, which significantly affects the efficiency of proteolytic digestion if an enzymatically active amino acid is adjacent to the N-linked glycosylation site. Proteolytic digestion then results in quantitatively different peptide products in accordance with the degree of glycosylation. The effect of glycan steric hindrance on tryptic digestion was first demonstrated using alpha-1-acid glycoprotein (AGP) as a model compound versus deglycosylated alpha-1-acid glycoprotein. Second, nonglycosylated tryptic peptide biomarkers, which generally show much higher sensitivity in mass spectrometric analyses than their glycosylated counterparts, were quantified in human hepatocellular carcinoma plasma using a label-free method with no need for N-linked glycoprotein enrichment. Finally, the method was validated using a multiple reaction monitoring analysis, demonstrating that the newly discovered nonglycosylated tryptic peptide targets were present at different levels in normal and hepatocellular carcinoma plasmas. The area under the receiver operating characteristic curve generated through analyses of nonglycosylated tryptic peptide from vitronectin precursor protein was 0.978, the highest observed in a group of patients with hepatocellular carcinoma. This work provides a targeted means of discovering and validating nonglycosylated tryptic peptides as biomarkers in human plasma, without the need for complex enrichment processes or expensive antibody preparations.",
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Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. / Lee, Ju Yeon; Kim, Jin Young; Park, Gun Wook; Cheon, Mi Hee; Kwon, Kyung Hoon; Ahn, Yeong Hee; Moon, Myeong Hee; Lee, Hyoung Joo; Paik, Young Ki; Yoo, Jong Shin.

In: Molecular & cellular proteomics : MCP, Vol. 10, No. 12, 01.12.2011.

Research output: Contribution to journalArticle

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AU - Park, Gun Wook

AU - Cheon, Mi Hee

AU - Kwon, Kyung Hoon

AU - Ahn, Yeong Hee

AU - Moon, Myeong Hee

AU - Lee, Hyoung Joo

AU - Paik, Young Ki

AU - Yoo, Jong Shin

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