2008 PUBLICATIONS 2007 PUBLICATIONS 2006 PUBLICATIONS 2005 PUBLICATIONS 2004 PUBLICATIONS

--------------------------------------------------------------------------------------------------------------

»2008 PUBLICATIONS

• Nadia Taouatas, Madalina M Drugan, Albert J R Heck & Shabaz Mohammed
Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase.
Nature Methods 2008, DOI:10.1038

• Maureen K. Bunger, Benjamin J. Cargile, Anne Ngunjiri, Jonathan L. Bundy,* and James L. Stephenson.
Automated Proteomics of E. coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry.
Anal. Chem. 2008, AC7018409

› Abstract:
This publication describes on-line LC MS analysis of intact proteins of E. coli lysate using advanced reaction chemistry (PTR). The interpretation of the resulting spectra with his own software leads to contiguous 17-amino acid readout of both N- and C-terminal sequences of the proteins.

back to top

----------------------------------------------------------------------------------

»2007 PUBLICATIONS

• Swaney, D. L.; McAlister, G. C.; Wirtala, M.; Schwartz, J. C.; Syka, J. E. P.; Coon, J. J.;
Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors;
Analytical Chemistry 2007, 79, 477-485.

› Abstract:
ETD, has shown limited applicability to doubly protonated peptide precursors, [M + 2H]2+, the charge and type of peptide most frequently encountered in “bottom-up” proteomics. Described here is a supplemental collisional activation (CAD) method that targets the nondissociated (intact) electron-transfer (ET) product species ([M + 2H]+¥) to improve ETD efficiency for doubly protonated peptides (ETcaD). A large-scale analysis of 755 doubly charged tryptic peptides was conducted to compare the method (ETcaD) to ion trap CAD and ETD.

• Chi, A.; Bai, D. L.; Geer, L. Y.; Shabanowitz, J.; Hunt, D. F.;
Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry;
International Journal of Mass Spectrometry 2007, 259, 197-203.

› Abstract:
Direct analysis of intact proteins on a chromatographic time scale is demonstrated on a modified linear ion trap mass spectrometer using sequential ion/ion reactions, electron transfer and proton transfer, to dissociate the sample and to convert the resulting peptide fragments to a mixture of singly and doubly charged species. Analysis of intact proteins from the Escherchia coli 70S ribosomal protein complex and identification of 46 of the 55 known unique components in a single, 90 min, on-line, chromatography experiment. Truncated versions of the above proteins along with several post-translational modifications are also detected.

• Swaney, D. L.; McAlister, G. C.; Wirtala, M.; Schwartz, J. C.; Syka, J. E. P.; Coon, J. J.;
Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors;
Analytical Chemistry 2007, 79, 477-485.

› Abstract:
ETD, has shown limited applicability to doubly protonated peptide precursors, [M + 2H]2+, the charge and type of peptide most frequently encountered in “bottom-up” proteomics. Described here is a supplemental collisional activation (CAD) method that targets the nondissociated (intact) electron-transfer (ET) product species ([M + 2H]+¥) to improve ETD efficiency for doubly protonated peptides (ETcaD). A large-scale analysis of 755 doubly charged tryptic peptides was conducted to compare the method (ETcaD) to ion trap CAD and ETD.

• Ueberheide, B. M.; Mollah, S.
International Journal of Mass Spectrometry 2007, 259, 46-56.

• Khidekel, N.; Ficarro, S., Clark, P., et al.
Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics;
Nature Chemical Biology 2007, 259, 46-56.

› Abstract:
Use of an LTQ XL with ETD to sequence O-GlcNAc-containing peptides and locate the exact sites of glycosylation.

• Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF.;
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2193-8. Epub 2007 Feb 7.

› Abstract:
Analysis of the yeast phosphoproteome that uses endo-Lys C as the proteolytic enzyme, immobilized metal affinity chromatography (IMAC) for phosphopeptide enrichment, a 90-min nanoflow-HPLC/electrospray-ionization MS/MS experiment for phosphopeptide fractionation and detection, gas phase ion/ion chemistry, ETD for peptide fragmentation. 1,252 phosphorylation sites on 629 proteins identified. Identified phosphoproteins have expression levels that range from<50 to 1,200,000 copies per cell and are encoded by genes involved in a wide variety of cellular processes.

• Taverna, Sean D., Ueberheide Beatrix M., Liu Yifan, Tackett Alan J., Diaz Robert L., Shabanowitz Jeffrey, Chait Brian T., Hunt Donald F, and Allis C. David;
Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini;
2086–2091;  PNAS; February 13, 2007; vol. 104; no. 7

› Abstract:
ETD/PTR used to determine combinatorial modification states on single, long N-terminal H3 fragments. The entire modification status of intact N termini was obtained and indicated correlations between K4 methylation and H3 acetylation. In addition, K4 and K27 methylation were identified concurrently on one H3 species.

• Good, D.M., Wirtala, M., McAlister, G., Coon, J.
Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry;
MCP.; August 2007.

• Wu, Shiaw-Lin.; Hühmer, A.; Hao, Z., Karger, B.
On-Line LC-MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications;
J. Proteome Res.; 2007.

• Chang, B., Chen, Y., Zhao, Y., Bruick, R.
JMJD6 Is a Histone Arginine Demethylase;
Science, 318; 444-447

• Namrata D. Udeshi, Jeffrey Shabanowitz, Donald F. Hunt and Kristie L. Rose
Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS;
FEBS Journal 2007, 274, 6269-6276.

› Abstract:
A mini-review with an overview of ETD application areas covered by recently published papers. It captures the main areas where the ETD technique comes across if not unique then at least highly complementary to CID – most of which were acquired using Thermo Scientific instrumentation.

• Sean D. Taverna, Beatrix M. Ueberheide, Yifan Liu, Alan J. Tackett, Robert L. Diaz, Jeffrey Shabanowitz, Brian T. Chait, Donald F. Hunt, and C. David Allis.
Long-distance combinatorial linkage between methylation and acetylation on histone H3 N-termini.
PNAS 2007, 104, 7, 2086–2091

› Abstract:
This reference may have the biggest impact for those interested in the analysis of PTMs. Here, the scientists focused on a certain type of histone molecule. The complex set of modifications on the N-terminal sequence of histones is responsible for switching gene transcription on and off. Some amino acids can carry multiple types of modifications, and the overall effect is dependent on the long-range connectivity of all of these. Using non-tryptic digest, the team purified the N-terminal subfraction of H3 molecules and analyzed them with LTQ ETD.

back to top

----------------------------------------------------------------------------------

»2006 PUBLICATIONS

• Good, D. M.; Coon, J. J.
Biotechniques 2006, 40, 783-789.

• Mikesh, L. M.; Ueberheide, B.; Chi, A.; Coon, J. J.; Syka, J. E. P.; Shabanowitz, J.; Hunt, D. F.
The utility of ETD mass spectrometry in proteomic analysis;
Biochimica Et Biophysica Acta-Proteins and Proteomics 2006, 1764, 1811-1822.

› Abstract:
The utility of electron transfer dissociation (ETD) mass spectrometry for sequence analysis of post-translationally modified and/or highly basic peptides is demonstrated. Phosphorylated, sulfonated, glycosylated, nitrosylated, disulfide bonded, methylated, acetylated, and highly basic peptides were analyzed by CAD and ETD mass spectrometry. CAD fragmentation typically produced spectra showing limited peptide backbone fragmentation. However, when these peptides were fragmented using ETD, peptide backbone fragmentation produced a complete or almost complete series of ions and thus extensive peptide sequence information. In addition, labile PTMs remained intact. These examples illustrate the utility of ETD as an advantageous tool in proteomic research by readily identifying peptides resistant to analysis by CAD. A further benefit is the ability to analyze larger, non-tryptic peptides, allowing for the detection of multiple PTMs within the context of one another.

back to top

----------------------------------------------------------------------------------

»2005 PUBLICATIONS

• Coon, J. J.; Syka, J. E.; Shabanowitz, J.; Hunt, D. F.
Biotechniques 2005, 38, 519, 521, 523.

• Coon, J. J.; Ueberheide, B.; Syka, J. E. P.; Dryhurst, D. D.; Ausio, J.; Shabanowitz, J.; Hunt, D. F.;
Protein identification using sequential ion/ion reactions and tandem mass spectrometry;.
Proceedings of the National Academy of Sciences of the United States of America 2005, 102, 9463-9468.
  › Available as free download from www.pnas.org

• Schroeder, M.J., Webb, D.J., Shabanowitz, J., Horwitz, A.F., and Hunt, D.F.;
Post-translational Modifications and Interacting Proteins by Mass Spectrometry: Methods for the Detection of Paxillin;
J. Proteome Res., 4, 5, 1832 - 1841, 2005

• Coon, J. J.; Shabanowitz, J.; Hunt, D. F.; Syka, J. E. P.
Journal of the American Society for Mass Spectrometry 2005, 16, 880-882.

• Coon, J. J.; Syka, J. E. P.; Shabanowitz, J.; Hunt, D. F.
Biotechniques 2005, 38, 519-+.

back to top

----------------------------------------------------------------------------------

»2004 PUBLICATIONS

• Syka, J. E. P.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F.;
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry;
PNAS 2004, 101, 9528-9533.
This original paper demonstrates the superiority of ETD on a linear (2D) ion trap.

› Abstract
Peptide sequence analysis using a combination of gas-phase ion-ion chemistry and tandem mass spectrometry (MS/MS) is demonstrated. Singly charged anthracene anions transfer an electron to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways that are analogous to those observed in electron capture dissociation. Modifications to the QLT that enable this ion-ion chemistry are presented, and automated acquisition of high-quality, single-scan electron transfer dissociation MS/MS spectra of phosphopeptides separated by nanoflow HPLC is described.

• Coon, J. J.; Syka, J. E. P.; Schwartz, J. C.; Shabanowitz, J.; Hunt, D. F.;
Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions;
International Journal of Mass Spectrometry 2004, 236, 33-42.

back to top