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Title: Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides

Abstract

Multiplex isobaric tags for relative and absolute quantification (iTRAQ) enable high-throughput quantification of peptides via reporter ion signals in the low mass range of tandem mass spectra. A challenging but highly promising application is to analyze iTRAQ-labeled peptides using a sensitive linear ion trap mass spectrometer (LTQ-MS) and pulsed Q dissociation (PQD), a form of ion trap collision activated dissociation (CAD) designed to allow detection of low mass-to-charge fragment ions. Electron dissociation transfer (ETD), on the other hand, is complementary to PQD and is especially useful for sequencing peptides containing post-translational modifications (PTMs). Here, we developed an integrated workflow for robust and accurate quantitative identification of iTRAQ labeled phosphopeptides that integrates the PQD and ETD fragmentation methods together with PQD optimization, data management and bioinformatics tools. Analysis of the phosphoproteome of human fibroblast cells demonstrated that this hybrid mode is superior to either PQD or ETD alone for phosphopeptide identification and quantitation. The combined PQD/ETD approach can qualitatively identify additional phosphopeptides than ETD alone and PQD information can provide better quantitation of ETD identified iTRAQ-labeled phosphopeptides.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
958485
Report Number(s):
PNNL-SA-63701
24698; 400412000; KP1602020; TRN: US201002%%56
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Analytical Chemistry, 81(10):4137-4143
Additional Journal Information:
Journal Volume: 81; Journal Issue: 10
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; DETECTION; DISSOCIATION; ELECTRON TRANSFER; FIBROBLASTS; MASS SPECTRA; PEPTIDES; ORGANIC PHOSPHORUS COMPOUNDS; IDENTIFICATION SYSTEMS; Environmental Molecular Sciences Laboratory

Citation Formats

Yang, Feng, Wu, Si, Stenoien, David L, Zhao, Rui, Monroe, Matthew E, Gritsenko, Marina A, Purvine, Samuel O, Polpitiya, Ashoka D, Tolic, Nikola, Zhang, Qibin, Norbeck, Angela D, Orton, Daniel J, Moore, Ronald J, Tang, Keqi, Anderson, Gordon A, Pasa-Tolic, Ljiljana, Camp, David G, and Smith, Richard D. Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides. United States: N. p., 2009. Web. doi:10.1021/ac802605m.
Yang, Feng, Wu, Si, Stenoien, David L, Zhao, Rui, Monroe, Matthew E, Gritsenko, Marina A, Purvine, Samuel O, Polpitiya, Ashoka D, Tolic, Nikola, Zhang, Qibin, Norbeck, Angela D, Orton, Daniel J, Moore, Ronald J, Tang, Keqi, Anderson, Gordon A, Pasa-Tolic, Ljiljana, Camp, David G, & Smith, Richard D. Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides. United States. doi:10.1021/ac802605m.
Yang, Feng, Wu, Si, Stenoien, David L, Zhao, Rui, Monroe, Matthew E, Gritsenko, Marina A, Purvine, Samuel O, Polpitiya, Ashoka D, Tolic, Nikola, Zhang, Qibin, Norbeck, Angela D, Orton, Daniel J, Moore, Ronald J, Tang, Keqi, Anderson, Gordon A, Pasa-Tolic, Ljiljana, Camp, David G, and Smith, Richard D. Fri . "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides". United States. doi:10.1021/ac802605m.
@article{osti_958485,
title = {Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides},
author = {Yang, Feng and Wu, Si and Stenoien, David L and Zhao, Rui and Monroe, Matthew E and Gritsenko, Marina A and Purvine, Samuel O and Polpitiya, Ashoka D and Tolic, Nikola and Zhang, Qibin and Norbeck, Angela D and Orton, Daniel J and Moore, Ronald J and Tang, Keqi and Anderson, Gordon A and Pasa-Tolic, Ljiljana and Camp, David G and Smith, Richard D},
abstractNote = {Multiplex isobaric tags for relative and absolute quantification (iTRAQ) enable high-throughput quantification of peptides via reporter ion signals in the low mass range of tandem mass spectra. A challenging but highly promising application is to analyze iTRAQ-labeled peptides using a sensitive linear ion trap mass spectrometer (LTQ-MS) and pulsed Q dissociation (PQD), a form of ion trap collision activated dissociation (CAD) designed to allow detection of low mass-to-charge fragment ions. Electron dissociation transfer (ETD), on the other hand, is complementary to PQD and is especially useful for sequencing peptides containing post-translational modifications (PTMs). Here, we developed an integrated workflow for robust and accurate quantitative identification of iTRAQ labeled phosphopeptides that integrates the PQD and ETD fragmentation methods together with PQD optimization, data management and bioinformatics tools. Analysis of the phosphoproteome of human fibroblast cells demonstrated that this hybrid mode is superior to either PQD or ETD alone for phosphopeptide identification and quantitation. The combined PQD/ETD approach can qualitatively identify additional phosphopeptides than ETD alone and PQD information can provide better quantitation of ETD identified iTRAQ-labeled phosphopeptides.},
doi = {10.1021/ac802605m},
journal = {Analytical Chemistry, 81(10):4137-4143},
number = 10,
volume = 81,
place = {United States},
year = {2009},
month = {5}
}