A simple carbamidomethylation-based isotope labeling method for quantitative shotgun proteomics

Donggeun Oh, Sun Young Lee, Meehyang Kwon, Sook Kyung Kim, Myeong Hee Moon, Dukjin Kang

Research output: Contribution to journalArticle

Abstract

In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as a complementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of all cysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively, leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification, 6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, and alpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. The resulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimental results, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobaric labeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variations in the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developed iCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study.

Original languageEnglish
Pages (from-to)63-69
Number of pages7
JournalMass Spectrometry Letters
Volume5
Issue number3
DOIs
Publication statusPublished - 2014 Jan 1

Fingerprint

Isotope Labeling
Firearms
Isotopes
Proteomics
Labeling
Iodoacetamide
Proteome
Peptides
Lactalbumin
Lactoglobulins
Proteins
Transferrin
beta-Galactosidase
Muramidase
Bovine Serum Albumin
Biomarkers
Digestion
Lung Neoplasms

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Spectroscopy

Cite this

Oh, Donggeun ; Lee, Sun Young ; Kwon, Meehyang ; Kim, Sook Kyung ; Moon, Myeong Hee ; Kang, Dukjin. / A simple carbamidomethylation-based isotope labeling method for quantitative shotgun proteomics. In: Mass Spectrometry Letters. 2014 ; Vol. 5, No. 3. pp. 63-69.
@article{f8efd68f18a444398b1ff6e167bad3c5,
title = "A simple carbamidomethylation-based isotope labeling method for quantitative shotgun proteomics",
abstract = "In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as a complementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of all cysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively, leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification, 6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, and alpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. The resulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimental results, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobaric labeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variations in the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developed iCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study.",
author = "Donggeun Oh and Lee, {Sun Young} and Meehyang Kwon and Kim, {Sook Kyung} and Moon, {Myeong Hee} and Dukjin Kang",
year = "2014",
month = "1",
day = "1",
doi = "10.5478/MSL.2014.5.3.63",
language = "English",
volume = "5",
pages = "63--69",
journal = "Mass Spectrometry Letters",
issn = "2233-4203",
publisher = "Korean Society Mass Spectrometry",
number = "3",

}

A simple carbamidomethylation-based isotope labeling method for quantitative shotgun proteomics. / Oh, Donggeun; Lee, Sun Young; Kwon, Meehyang; Kim, Sook Kyung; Moon, Myeong Hee; Kang, Dukjin.

In: Mass Spectrometry Letters, Vol. 5, No. 3, 01.01.2014, p. 63-69.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A simple carbamidomethylation-based isotope labeling method for quantitative shotgun proteomics

AU - Oh, Donggeun

AU - Lee, Sun Young

AU - Kwon, Meehyang

AU - Kim, Sook Kyung

AU - Moon, Myeong Hee

AU - Kang, Dukjin

PY - 2014/1/1

Y1 - 2014/1/1

N2 - In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as a complementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of all cysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively, leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification, 6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, and alpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. The resulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimental results, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobaric labeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variations in the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developed iCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study.

AB - In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as a complementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of all cysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively, leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification, 6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, and alpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. The resulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimental results, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobaric labeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variations in the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developed iCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study.

UR - http://www.scopus.com/inward/record.url?scp=84907812205&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84907812205&partnerID=8YFLogxK

U2 - 10.5478/MSL.2014.5.3.63

DO - 10.5478/MSL.2014.5.3.63

M3 - Article

VL - 5

SP - 63

EP - 69

JO - Mass Spectrometry Letters

JF - Mass Spectrometry Letters

SN - 2233-4203

IS - 3

ER -