Literature DB >> 24178922

Neutron-encoded protein quantification by peptide carbamylation.

Arne Ulbrich1, Anna E Merrill, Alexander S Hebert, Michael S Westphall, Mark P Keller, Alan D Attie, Joshua J Coon.   

Abstract

We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression in mice fed a either control or high-fat diet.

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Year:  2013        PMID： 24178922      PMCID： PMC3880647          DOI： 10.1007/s13361-013-0765-z

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN： 1044-0305            Impact factor:   3.109


  14 in total

1.  Open mass spectrometry search algorithm.

Authors:  Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

2.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors:  Joshua E Elias; Steven P Gygi
Journal:  Nat Methods       Date:  2007-03       Impact factor: 28.547

Review 3.  Quantitative mass spectrometry in proteomics: a critical review.

Authors:  Marcus Bantscheff; Markus Schirle; Gavain Sweetman; Jens Rick; Bernhard Kuster
Journal:  Anal Bioanal Chem       Date:  2007-08-01       Impact factor: 4.142

4.  Value of using multiple proteases for large-scale mass spectrometry-based proteomics.

Authors:  Danielle L Swaney; Craig D Wenger; Joshua J Coon
Journal:  J Proteome Res       Date:  2010-03-05       Impact factor: 4.466

5.  Induction of peroxisomal lipid metabolism in mice fed a high-fat diet.

Authors:  Sachi Kozawa; Ayako Honda; Naomi Kajiwara; Yasuhiko Takemoto; Tomoko Nagase; Hideki Nikami; Yukio Okano; Shigeru Nakashima; Nobuyuki Shimozawa
Journal:  Mol Med Rep       Date:  2011-08-17       Impact factor: 2.952

6.  COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA.

Authors:  Craig D Wenger; Douglas H Phanstiel; M Violet Lee; Derek J Bailey; Joshua J Coon
Journal:  Proteomics       Date:  2011-02-07       Impact factor: 3.984

7.  Tools for glycomics: relative quantitation of glycans by isotopic permethylation using 13CH3I.

Authors:  Gerardo Alvarez-Manilla; Nicole Lynn Warren; Trina Abney; James Atwood; Parastoo Azadi; Will S York; Michael Pierce; Ron Orlando
Journal:  Glycobiology       Date:  2007-03-23       Impact factor: 4.313

8.  A high-fat diet coordinately downregulates genes required for mitochondrial oxidative phosphorylation in skeletal muscle.

Authors:  Lauren M Sparks; Hui Xie; Robert A Koza; Randall Mynatt; Matthew W Hulver; George A Bray; Steven R Smith
Journal:  Diabetes       Date:  2005-07       Impact factor: 9.461

9.  Quantitative carbamylation as a stable isotopic labeling method for comparative proteomics.

Authors:  Peggi M Angel; Ron Orlando
Journal:  Rapid Commun Mass Spectrom       Date:  2007       Impact factor: 2.419

10.  Neutron-encoded mass signatures for multiplexed proteome quantification.

Authors:  Alexander S Hebert; Anna E Merrill; Derek J Bailey; Amelia J Still; Michael S Westphall; Eric R Strieter; David J Pagliarini; Joshua J Coon
Journal:  Nat Methods       Date:  2013-02-24       Impact factor: 28.547
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  10 in total

1.  Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis.

Authors:  Christoph Hage; Francesco Falvo; Mathias Schäfer; Andrea Sinz
Journal:  J Am Soc Mass Spectrom       Date:  2017-06-26       Impact factor: 3.109

2.  NeuCode labels for relative protein quantification.

Authors:  Anna E Merrill; Alexander S Hebert; Matthew E MacGilvray; Christopher M Rose; Derek J Bailey; Joel C Bradley; William W Wood; Marwan El Masri; Michael S Westphall; Audrey P Gasch; Joshua J Coon
Journal:  Mol Cell Proteomics       Date:  2014-06-17       Impact factor: 5.911

3.  NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans.

Authors:  Timothy W Rhoads; Aman Prasad; Nicholas W Kwiecien; Anna E Merrill; Kelson Zawack; Michael S Westphall; Frank C Schroeder; Judith Kimble; Joshua J Coon
Journal:  Mol Cell Proteomics       Date:  2015-09-21       Impact factor: 5.911

4.  Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics.

Authors:  Dustin C Frost; Tyler Greer; Feng Xiang; Zhidan Liang; Lingjun Li
Journal:  Rapid Commun Mass Spectrom       Date:  2015-06-30       Impact factor: 2.419

5.  High-throughput bioconjugation for enhanced 193 nm photodissociation via droplet phase initiated ion/ion chemistry using a front-end dual spray reactor.

Authors:  Victoria C Cotham; Jared B Shaw; Jennifer S Brodbelt
Journal:  Anal Chem       Date:  2015-08-31       Impact factor: 6.986

6.  Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents.

Authors:  Scott B Ficarro; Jessica M Biagi; Jinhua Wang; Jenna Scotcher; Rositsa I Koleva; Joseph D Card; Guillaume Adelmant; Huan He; Manor Askenazi; Alan G Marshall; Nicolas L Young; Nathanael S Gray; Jarrod A Marto
Journal:  J Am Soc Mass Spectrom       Date:  2014-02-05       Impact factor: 3.109

7.  Neucode Labels for Multiplexed, Absolute Protein Quantification.

Authors:  Gregory K Potts; Emily A Voigt; Derek J Bailey; Christopher M Rose; Michael S Westphall; Alexander S Hebert; John Yin; Joshua J Coon
Journal:  Anal Chem       Date:  2016-02-25       Impact factor: 6.986

Review 8.  Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity.

Authors:  Theo Klein; Rosa I Viner; Christopher M Overall
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-10-28       Impact factor: 4.226

9.  Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS).

Authors:  Tyler Greer; Ling Hao; Anatoliy Nechyporenko; Sanghee Lee; Chad M Vezina; Will A Ricke; Paul C Marker; Dale E Bjorling; Wade Bushman; Lingjun Li
Journal:  PLoS One       Date:  2015-08-12       Impact factor: 3.240

Review 10.  Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling.

Authors:  Nicholas M Riley; Joshua J Coon
Journal:  Anal Chem       Date:  2015-11-19       Impact factor: 6.986
  10 in total

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