MCP AbD Serotec
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Originally published In Press as doi:10.1074/mcp.T400003-MCP200 on March 19, 2004.
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Data
Right arrow All Versions of this Article:
T400003-MCP200v1
3/6/608    most recent
Right arrow Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when eLetters are posted
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow Glossary
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Olsen, J. V.
Right arrow Articles by Mann, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Olsen, J. V.
Right arrow Articles by Mann, M.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Molecular & Cellular Proteomics 3:608-614, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues*,S

Jesper V. Olsen, Shao-En Ong and Matthias Mann{ddagger}

From the Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark

Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert protein mixtures into more readily analyzable peptide populations. When searching peptide fragmentation spectra against sequence databases, potentially matching peptide sequences can be required to conform to tryptic specificity, namely, cleavage exclusively C-terminal to arginine or lysine. In many published reports, however, significant numbers of proteins are identified by non-tryptic peptides. Here we use the sub-parts per million mass accuracy of a new ion trap Fourier transform mass spectrometer to achieve more than a 100-fold increased confidence in peptide identification compared with typical ion trap experiments and show that trypsin cleaves solely C-terminal to arginine and lysine. We find that non-tryptic peptides occur only as the C-terminal peptides of proteins and as breakup products of fully tryptic peptides N-terminal to an internal proline. Simulating lower mass accuracy led to a large number of proteins erroneously identified with non-tryptic peptide hits. Our results indicate that such peptide hits in previous studies should be re-examined and that peptide identification should be based on strict trypsin specificity.

{ddagger} To whom correspondence should be addressed: Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. Tel.: 45-6550-2364; Fax: 45-6539- 3929; E-mail: mann{at}bmb.sdu.dk


Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Mol. Cell. ProteomicsHome page
L. F. Waanders, R. Almeida, S. Prosser, J. Cox, D. Eikel, M. H. Allen, G. A. Schultz, and M. Mann
A Novel Chromatographic Method Allows On-line Reanalysis of the Proteome
Mol. Cell. Proteomics, August 1, 2008; 7(8): 1452 - 1459.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
M. Rogalski, M. A. Schottler, W. Thiele, W. X. Schulze, and R. Bock
Rpl33, a Nonessential Plastid-Encoded Ribosomal Protein in Tobacco, Is Required under Cold Stress Conditions
PLANT CELL, August 1, 2008; 20(8): 2221 - 2237.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
K. Nordick, M. G. Hoffman, J. L. Betz, and J. A. Jaehning
Direct Interactions between the Paf1 Complex and a Cleavage and Polyadenylation Factor Are Revealed by Dissociation of Paf1 from RNA Polymerase II
Eukaryot. Cell, July 1, 2008; 7(7): 1158 - 1167.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
B. Shin, H.-J. Jung, S.-W. Hyung, H. Kim, D. Lee, C. Lee, M.-H. Yu, and S.-W. Lee
Postexperiment Monoisotopic Mass Filtering and Refinement (PE-MMR) of Tandem Mass Spectrometric Data Increases Accuracy of Peptide Identification in LC/MS/MS
Mol. Cell. Proteomics, June 1, 2008; 7(6): 1124 - 1134.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. Graumann, N. C. Hubner, J. B. Kim, K. Ko, M. Moser, C. Kumar, J. Cox, H. Scholer, and M. Mann
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins
Mol. Cell. Proteomics, April 1, 2008; 7(4): 672 - 683.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
S. Haase, A. Cabrera, C. Langer, M. Treeck, N. Struck, S. Herrmann, P. W. Jansen, I. Bruchhaus, A. Bachmann, S. Dias, et al.
Characterization of a Conserved Rhoptry-Associated Leucine Zipper-Like Protein in the Malaria Parasite Plasmodium falciparum
Infect. Immun., March 1, 2008; 76(3): 879 - 887.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
T. W. Loehfelm, N. R. Luke, and A. A. Campagnari
Identification and Characterization of an Acinetobacter baumannii Biofilm-Associated Protein
J. Bacteriol., February 1, 2008; 190(3): 1036 - 1044.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
I. Matic, M. van Hagen, J. Schimmel, B. Macek, S. C. Ogg, M. H. Tatham, R. T. Hay, A. I. Lamond, M. Mann, and A. C. O. Vertegaal
In Vivo Identification of Human Small Ubiquitin-like Modifier Polymerization Sites by High Accuracy Mass Spectrometry and an in Vitro to in Vivo Strategy
Mol. Cell. Proteomics, January 1, 2008; 7(1): 132 - 144.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Alves, R. J. Arnold, D. E. Clemmer, Y. Li, J. P. Reilly, Q. Sheng, H. Tang, Z. Xun, R. Zeng, and P. Radivojac
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Bioinformatics, January 1, 2008; 24(1): 102 - 109.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. Wiese, T. Gronemeyer, R. Ofman, M. Kunze, C. P. Grou, J. A. Almeida, M. Eisenacher, C. Stephan, H. Hayen, L. Schollenberger, et al.
Proteomics Characterization of Mouse Kidney Peroxisomes by Tandem Mass Spectrometry and Protein Correlation Profiling
Mol. Cell. Proteomics, December 1, 2007; 6(12): 2045 - 2057.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
P. Picotti, R. Aebersold, and B. Domon
The Implications of Proteolytic Background for Shotgun Proteomics
Mol. Cell. Proteomics, September 1, 2007; 6(9): 1589 - 1598.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
N. Gupta, S. Tanner, N. Jaitly, J. N. Adkins, M. Lipton, R. Edwards, M. Romine, A. Osterman, V. Bafna, R. D. Smith, et al.
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Genome Res., September 1, 2007; 17(9): 1362 - 1377.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. Falth, K. Skold, M. Svensson, A. Nilsson, D. Fenyo, and P. E. Andren
Neuropeptidomics Strategies for Specific and Sensitive Identification of Endogenous Peptides
Mol. Cell. Proteomics, July 1, 2007; 6(7): 1188 - 1197.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. Adachi, C. Kumar, Y. Zhang, and M. Mann
In-depth Analysis of the Adipocyte Proteome by Mass Spectrometry and Bioinformatics
Mol. Cell. Proteomics, July 1, 2007; 6(7): 1257 - 1273.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
N. Sugiyama, T. Masuda, K. Shinoda, A. Nakamura, M. Tomita, and Y. Ishihama
Phosphopeptide Enrichment by Aliphatic Hydroxy Acid-modified Metal Oxide Chromatography for Nano-LC-MS/MS in Proteomics Applications
Mol. Cell. Proteomics, June 1, 2007; 6(6): 1103 - 1109.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
B. Macek, I. Mijakovic, J. V. Olsen, F. Gnad, C. Kumar, P. R. Jensen, and M. Mann
The Serine/Threonine/Tyrosine Phosphoproteome of the Model Bacterium Bacillus subtilis
Mol. Cell. Proteomics, April 1, 2007; 6(4): 697 - 707.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
R. Zubarev and M. Mann
On the Proper Use of Mass Accuracy in Proteomics
Mol. Cell. Proteomics, March 1, 2007; 6(3): 377 - 381.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Zhang, Y. Zhang, J. Adachi, J. V. Olsen, R. Shi, G. de Souza, E. Pasini, L. J. Foster, B. Macek, A. Zougman, et al.
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D771 - D779.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
Q. W. T. Chan, C. G. Howes, and L. J. Foster
Quantitative Comparison of Caste Differences in Honeybee Hemolymph
Mol. Cell. Proteomics, December 1, 2006; 5(12): 2252 - 2262.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. L. Nielsen, M. M. Savitski, and R. A. Zubarev
Extent of Modifications in Human Proteome Samples and Their Effect on Dynamic Range of Analysis in Shotgun Proteomics
Mol. Cell. Proteomics, December 1, 2006; 5(12): 2384 - 2391.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
M. Vermeulen, W. Walter, X. Le Guezennec, J. Kim, R. S. Edayathumangalam, E. Lasonder, K. Luger, R. G. Roeder, C. Logie, S. L. Berger, et al.
A Feed-Forward Repression Mechanism Anchors the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressors on Chromatin.
Mol. Cell. Biol., July 1, 2006; 26(14): 5226 - 5236.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
D. L. Alexander, S. Arastu-Kapur, J.-F. Dubremetz, and J. C. Boothroyd
Plasmodium falciparum AMA1 Binds a Rhoptry Neck Protein Homologous to TgRON4, a Component of the Moving Junction in Toxoplasma gondii.
Eukaryot. Cell, July 1, 2006; 5(7): 1169 - 1173.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
W. Haas, B. K. Faherty, S. A. Gerber, J. E. Elias, S. A. Beausoleil, C. E. Bakalarski, X. Li, J. Villen, and S. P. Gygi
Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics
Mol. Cell. Proteomics, July 1, 2006; 5(7): 1326 - 1337.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. C. Dieterich, A. J. Link, J. Graumann, D. A. Tirrell, and E. M. Schuman
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)
PNAS, June 20, 2006; 103(25): 9482 - 9487.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. M. Savitski, M. L. Nielsen, and R. A. Zubarev
ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures
Mol. Cell. Proteomics, May 1, 2006; 5(5): 935 - 948.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
F. Forner, L. J. Foster, S. Campanaro, G. Valle, and M. Mann
Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver
Mol. Cell. Proteomics, April 1, 2006; 5(4): 608 - 619.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Mijakovic, D. Petranovic, B. Macek, T. Cepo, M. Mann, J. Davies, P. R. Jensen, and D. Vujaklija
Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine
Nucleic Acids Res., March 20, 2006; 34(5): 1588 - 1596.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
X. Le Guezennec, M. Vermeulen, A. B. Brinkman, W. A. M. Hoeijmakers, A. Cohen, E. Lasonder, and H. G. Stunnenberg
MBD2/NuRD and MBD3/NuRD, Two Distinct Complexes with Different Biochemical and Functional Properties
Mol. Cell. Biol., February 1, 2006; 26(3): 843 - 851.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
G. Zhang and T. A. Neubert
Automated Comparative Proteomics Based on Multiplex Tandem Mass Spectrometry and Stable Isotope Labeling
Mol. Cell. Proteomics, February 1, 2006; 5(2): 401 - 411.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. V. Olsen, L. M. F. de Godoy, G. Li, B. Macek, P. Mortensen, R. Pesch, A. Makarov, O. Lange, S. Horning, and M. Mann
Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap
Mol. Cell. Proteomics, December 1, 2005; 4(12): 2010 - 2021.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. E. McBride, J. T. Cook, E. A. Stemmler, K. L. Rutledge, K. A. McGrath, and J. A. Rubens
Arginine Methylation of Yeast mRNA-binding Protein Npl3 Directly Affects Its Function, Nuclear Export, and Intranuclear Protein Interactions
J. Biol. Chem., September 2, 2005; 280(35): 30888 - 30898.
[Abstract] [Full Text] [PDF]

Home page
 Stem CellsHome page
L. J. Foster, P. A. Zeemann, C. Li, M. Mann, O. N. Jensen, and M. Kassem
Differential Expression Profiling of Membrane Proteins by Quantitative Proteomics in a Human Mesenchymal Stem Cell Line Undergoing Osteoblast Differentiation
Stem Cells, September 1, 2005; 23(9): 1367 - 1377.
[Abstract] [Full Text] [PDF]

Home page
 J. Lipid Res.Home page
C. Yu, M. Alterman, and R. T. Dobrowsky
Ceramide displaces cholesterol from lipid rafts and decreases the association of the cholesterol binding protein caveolin-1
J. Lipid Res., August 1, 2005; 46(8): 1678 - 1691.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. X. Andersson, K. E. Larsson, H. Tjellstrom, C. Liljenberg, and A. S. Sandelius
Phosphate-limited Oat: THE PLASMA MEMBRANE AND THE TONOPLAST AS MAJOR TARGETS FOR PHOSPHOLIPID-TO-GLYCOLIPID REPLACEMENT AND STIMULATION OF PHOSPHOLIPASES IN THE PLASMA MEMBRANE
J. Biol. Chem., July 29, 2005; 280(30): 27578 - 27586.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. L. Nielsen, M. M. Savitski, and R. A. Zubarev
Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry
Mol. Cell. Proteomics, June 1, 2005; 4(6): 835 - 845.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
H. Molina, J. Bunkenborg, G. H. Reddy, B. Muthusamy, P. J. Scheel, and A. Pandey
A Proteomic Analysis of Human Hemodialysis Fluid
Mol. Cell. Proteomics, May 1, 2005; 4(5): 637 - 650.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
P. Aa. Nielsen, J. V. Olsen, A. V. Podtelejnikov, J. R. Andersen, M. Mann, and J. R. Wisniewski
Proteomic Mapping of Brain Plasma Membrane Proteins
Mol. Cell. Proteomics, April 1, 2005; 4(4): 402 - 408.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
A. Gruhler, J. V. Olsen, S. Mohammed, P. Mortensen, N. J. Faergeman, M. Mann, and O. N. Jensen
Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway
Mol. Cell. Proteomics, March 1, 2005; 4(3): 310 - 327.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. M. Hinsby, J. V. Olsen, and M. Mann
Tyrosine Phosphoproteomics of Fibroblast Growth Factor Signaling: A ROLE FOR INSULIN RECEPTOR SUBSTRATE-4
J. Biol. Chem., November 5, 2004; 279(45): 46438 - 46447.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. V. Olsen and M. Mann
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation
PNAS, September 14, 2004; 101(37): 13417 - 13422.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
 All ASBMB Journals   Journal of Biological Chemistry 
 Journal of Lipid Research   ASBMB Today 
Copyright © 2004 by the American Society for Biochemistry and Molecular Biology.