Quantitative proteomics for identification of cancer biomarkers

Raghothama Chaerkady, Akhilesh Pandey

Research output: Contribution to journalArticle

Abstract

Quantitative proteomics can be used for the identification of cancer biomarkers that could be used or early detection, serve as therapeutic targets, or monitor response to treatment. Several quantitative proteomics tools are currently available to study differential expression of proteins in samples ranging from cancer cell lines to tissues to body fluids. 2-DE, which was classically used for proteomic profiling, has been coupled to fluorescence labeling for differential proteomics. Isotope labeling methods such as stable isotope labeling with amino acids in cell culture (SILAC), isotope-coded affinity tagging (ICAT), isobaric tags for relative and absolute quantitation (iTRAQ), and 18O labeling have all been used in quantitative approaches for identification of cancer biomarkers. In addition, heavy isotope labeled peptides can be used to obtain absolute quantitative data. Most recently, label-free methods for quantitative proteomics, which have the potential of replacing isotope-labeling strategies, are becoming popular. other emerging technologies such as protein microarrays have the potential for providing additional opportunities for biomarker identification. This review highlights commonly used methods for quantitative proteomic analysis and their advantages and limitations for cancer biomarker analysis.

Original languageEnglish (US)
Pages (from-to)1080-1089
Number of pages10
JournalProteomics - Clinical Applications
Volume1
Issue number9
DOIs
StatePublished - Sep 2007

Fingerprint

Tumor Biomarkers
Proteomics
Isotope Labeling
Isotopes
Labeling
Protein Array Analysis
Body fluids
Body Fluids
Biomarkers
Microarrays
Cell culture
Labels
Proteins
Cell Culture Techniques
Fluorescence
Cells
Tissue
Technology
Amino Acids
Cell Line

Keywords

  • Multiplexing
  • Screening
  • Stable isotope labeling
  • Validation

ASJC Scopus subject areas

  • Clinical Biochemistry

Cite this

Quantitative proteomics for identification of cancer biomarkers. / Chaerkady, Raghothama; Pandey, Akhilesh.

In: Proteomics - Clinical Applications, Vol. 1, No. 9, 09.2007, p. 1080-1089.

Research output: Contribution to journalArticle

Chaerkady, Raghothama ; Pandey, Akhilesh. / Quantitative proteomics for identification of cancer biomarkers. In: Proteomics - Clinical Applications. 2007 ; Vol. 1, No. 9. pp. 1080-1089.
@article{33adf8ae9ce84d41b0321551bd5518ef,
title = "Quantitative proteomics for identification of cancer biomarkers",
abstract = "Quantitative proteomics can be used for the identification of cancer biomarkers that could be used or early detection, serve as therapeutic targets, or monitor response to treatment. Several quantitative proteomics tools are currently available to study differential expression of proteins in samples ranging from cancer cell lines to tissues to body fluids. 2-DE, which was classically used for proteomic profiling, has been coupled to fluorescence labeling for differential proteomics. Isotope labeling methods such as stable isotope labeling with amino acids in cell culture (SILAC), isotope-coded affinity tagging (ICAT), isobaric tags for relative and absolute quantitation (iTRAQ), and 18O labeling have all been used in quantitative approaches for identification of cancer biomarkers. In addition, heavy isotope labeled peptides can be used to obtain absolute quantitative data. Most recently, label-free methods for quantitative proteomics, which have the potential of replacing isotope-labeling strategies, are becoming popular. other emerging technologies such as protein microarrays have the potential for providing additional opportunities for biomarker identification. This review highlights commonly used methods for quantitative proteomic analysis and their advantages and limitations for cancer biomarker analysis.",
keywords = "Multiplexing, Screening, Stable isotope labeling, Validation",
author = "Raghothama Chaerkady and Akhilesh Pandey",
year = "2007",
month = "9",
doi = "10.1002/prca.200700284",
language = "English (US)",
volume = "1",
pages = "1080--1089",
journal = "Proteomics - Clinical Applications",
issn = "1862-8346",
publisher = "Wiley-VCH Verlag",
number = "9",

}

TY - JOUR

T1 - Quantitative proteomics for identification of cancer biomarkers

AU - Chaerkady, Raghothama

AU - Pandey, Akhilesh

PY - 2007/9

Y1 - 2007/9

N2 - Quantitative proteomics can be used for the identification of cancer biomarkers that could be used or early detection, serve as therapeutic targets, or monitor response to treatment. Several quantitative proteomics tools are currently available to study differential expression of proteins in samples ranging from cancer cell lines to tissues to body fluids. 2-DE, which was classically used for proteomic profiling, has been coupled to fluorescence labeling for differential proteomics. Isotope labeling methods such as stable isotope labeling with amino acids in cell culture (SILAC), isotope-coded affinity tagging (ICAT), isobaric tags for relative and absolute quantitation (iTRAQ), and 18O labeling have all been used in quantitative approaches for identification of cancer biomarkers. In addition, heavy isotope labeled peptides can be used to obtain absolute quantitative data. Most recently, label-free methods for quantitative proteomics, which have the potential of replacing isotope-labeling strategies, are becoming popular. other emerging technologies such as protein microarrays have the potential for providing additional opportunities for biomarker identification. This review highlights commonly used methods for quantitative proteomic analysis and their advantages and limitations for cancer biomarker analysis.

AB - Quantitative proteomics can be used for the identification of cancer biomarkers that could be used or early detection, serve as therapeutic targets, or monitor response to treatment. Several quantitative proteomics tools are currently available to study differential expression of proteins in samples ranging from cancer cell lines to tissues to body fluids. 2-DE, which was classically used for proteomic profiling, has been coupled to fluorescence labeling for differential proteomics. Isotope labeling methods such as stable isotope labeling with amino acids in cell culture (SILAC), isotope-coded affinity tagging (ICAT), isobaric tags for relative and absolute quantitation (iTRAQ), and 18O labeling have all been used in quantitative approaches for identification of cancer biomarkers. In addition, heavy isotope labeled peptides can be used to obtain absolute quantitative data. Most recently, label-free methods for quantitative proteomics, which have the potential of replacing isotope-labeling strategies, are becoming popular. other emerging technologies such as protein microarrays have the potential for providing additional opportunities for biomarker identification. This review highlights commonly used methods for quantitative proteomic analysis and their advantages and limitations for cancer biomarker analysis.

KW - Multiplexing

KW - Screening

KW - Stable isotope labeling

KW - Validation

UR - http://www.scopus.com/inward/record.url?scp=38349159301&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38349159301&partnerID=8YFLogxK

U2 - 10.1002/prca.200700284

DO - 10.1002/prca.200700284

M3 - Article

C2 - 21136759

AN - SCOPUS:38349159301

VL - 1

SP - 1080

EP - 1089

JO - Proteomics - Clinical Applications

JF - Proteomics - Clinical Applications

SN - 1862-8346

IS - 9

ER -