Bilbliography for chapter 1,2,7 and Extended Abstracts Aebersold, R. & Mann, M.
Mass spectrometry-based proteomics.
Nature,
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA.
raebersold@systemsbiology.org, 2003, 422, 198-207
Anderson, D. C.; Li, W.; Payan, D. G. & Noble, W. S.
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores.
J Proteome Res,
Rigel Incorporated, 240 East Grand Avenue, South San Francisco, California 94080, USA.
dca0210@earthlink.net, 2003, 2, 137-146 Baldwin, M. A.
Protein identification by mass spectrometry: issues to be considered.
Mol Cell Proteomics,
Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, USA. mikeab@itsa.ucsf.edu, 2004, 3, 1-9
Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villén, J.; Li, J.; Cohn, M. A.;
Cantley, L. C. & Gygi, S. P.
Large-scale characterization of HeLa cell nuclear phosphoproteins.
Proc Natl Acad Sci U S A, 2004, 101, 12130-12135
Binz, P. A.; Müller, M.; Walther, D.; Bienvenut, W. V.; Gras, R.; Hoogland, C.; Bouchet, G.;
Gasteiger, E.; Fabbretti, R.; Gay, S.; Palagi, P.; Wilkins, M. R.; Rouge, V.; Tonella, L.;
Paesano, S.; Rossellat, G.; Karmime, A.; Bairoch, A.; Sanchez, J. C.; Appel, R. D. &
Hochstrasser, D. F.
A molecular scanner to automate proteomic research and to display proteome images.
Anal Chem,
Swiss Institute of Bioinformatics, University Medical Center, Geneva, Switzerland. Pierre-Alain.Binz@dim.hcuge.ch, 1999, 71, 4981-4988
Bodenmiller, B.; Campbell, D.; Gerrits, B.; Lam, H.; Jovanovic, M.; Picotti, P.; Schlapbach, R. & Aebersold, R.
PhosphoPep--a database of protein phosphorylation sites in model organisms.
Nat Biotechnol, 2008, 26, 1339-1340
Bodenmiller, B.; Malmstrom, J.; Gerrits, B.; Campbell, D.; Lam, H.; Schmidt, A.; Rinner, O.;
Mueller, L. N.; Shannon, P. T.; Pedrioli, P. G.; Panse, C.; Lee, H.; Schlapbach, R. &
Aebersold, R.
PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.
Mol Syst Biol,
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., 2007, 3, 139 Bodenmiller, B.; Mueller, L. N.; Mueller, M.; Domon, B. & Aebersold, R.
Reproducible isolation of distinct, overlapping segments of the phosphoproteome.
Nat Methods,
Institute for Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Hönggerberg, Wolfgang-Pauli-Str. 16, HPT, CH-8093 Zürich, Switzerland., 2007, 4, 231-237 Brunner, E.; Ahrens, C. H.; Mohanty, S.; Baetschmann, H.; Loevenich, S.; Potthast, F.;
Deutsch, E. W.; Panse, C.; de Lichtenberg, U.; Rinner, O.; Lee, H.; Pedrioli, P. G. A.;
Malmstrom, J.; Koehler, K.; Schrimpf, S.; Krijgsveld, J.; Kregenow, F.; Heck, A. J. R.; Hafen, E.; Schlapbach, R. & Aebersold, R.
A high-quality catalog of the Drosophila melanogaster proteome.
Nat Biotechnol,
Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. erich.brunner@molbio.uzh.ch, 2007, 25, 576-583
174 Carr, S.; Aebersold, R.; Baldwin, M.; Burlingame, A.; Clauser, K.; Nesvizhskii, A.; on Publication Guidelines for Peptide, W. G. & Data, P. I.
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.
Mol Cell Proteomics, 2004, 3, 531-533
Chi, A.; Huttenhower, C.; Geer, L. Y.; Coon, J. J.; Syka, J. E. P.; Bai, D. L.; Shabanowitz, J.;
Burke, D. J.; Troyanskaya, O. G. & Hunt, D. F.
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.
Proc Natl Acad Sci U S A, 2007, 104, 2193-2198
Clauser, K. R.; Hall, S. C.; Smith, D. M.; Webb, J. W.; Andrews, L. E.; Tran, H. M.; Epstein, L. B. & Burlingame, A. L.
Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE.
Proc Natl Acad Sci U S A,
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA., 1995, 92, 5072-5076
Colinge, J.; Masselot, A.; Giron, M.; Dessingy, T. & Magnin, J.
OLAV: towards high-throughput tandem mass spectrometry data identification.
Proteomics,
2003, 3, 1454-1463
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.
Proc Natl Acad Sci U S A, 2005, 102, 9463-9468
Craig, R.; Cortens, J. C.; Fenyo, D. & Beavis, R. C.
Using annotated peptide mass spectrum libraries for protein identification.
J Proteome Res, 2006, 5, 1843-1849
Creasy, D. M. & Cottrell, J. S.
Unimod: Protein modifications for mass spectrometry.
Proteomics,
2004, 4, 1534-1536
Dancík, V.; Addona, T. A.; Clauser, K. R.; Vath, J. E. & Pevzner, P. A.
De novo peptide sequencing via tandem mass spectrometry.
J Comput Biol,
Millennium Pharmaceuticals, Cambridge, Massachusetts 02139, USA. dancik@mpi.com, 1999, 6, 327-342
Eng, J. K.; McCormack, A. L. & III, J. R. Y.
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
Journal of the American Society for Mass Spectrometry, 1994, 5, 976 - 989
Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F. & Whitehouse, C. M.
Electrospray ionization for mass spectrometry of large biomolecules.
Science,
Chemical Engineering Department, Yale University, New Haven, CT 06520., 1989, 246, 64-71
Fernandez-de-Cossio, J.; Gonzalez, J.; Satomi, Y.; Shima, T.; Okumura, N.; Besada, V.;
Betancourt, L.; Padron, G.; Shimonishi, Y. & Takao, T.
Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry.
176 Electrophoresis,
2000, 21, 1694-1699
Ficarro, S. B.; McCleland, M. L.; Stukenberg, P. T.; Burke, D. J.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F. & White, F. M.
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.
Nat Biotechnol, 2002, 20, 301-305
Frank, A. & Pevzner, P.
PepNovo: de novo peptide sequencing via probabilistic network modeling.
Anal Chem, 2005, 77, 964-973
Frewen, B. E.; Merrihew, G. E.; Wu, C. C.; Noble, W. S. & MacCoss, M. J.
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.
Anal Chem,
2006, 78, 5678-5684
Geiser, L.; Dayon, L.; Vaezzadeh, A. R. & Hochstrasser, D. F.
Shotgun proteomics: a relative quantitative approach using Off-Gel electrophoresis and LC-MS/MS.
Methods Mol Biol,
Swiss Centre for Applied Human Toxicology, Geneva University, Geneva, Switzerland., 2011, 681, 459-472
Heller, M.; Michel, P. E.; Morier, P.; Crettaz, D.; Wenz, C.; Tissot, J.; Reymond, F. & Rossier, J. S.
Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma.
Electrophoresis,
DiagnoSwiss SA, CH-1870 Monthey, Switzerland., 2005, 26, 1174-1188
Henzel, W. J.; Billeci, T. M.; Stults, J. T.; Wong, S. C.; Grimley, C. & Watanabe, C.
Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases.
Proc Natl Acad Sci U S A,
Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA 94080-4990., 1993, 90, 5011-5015
Henzel, W. J.; Watanabe, C. & Stults, J. T.
Protein identification: the origins of peptide mass fingerprinting.
J Am Soc Mass Spectrom,
Protein Chemistry Department and Bioinformatics Department, Genentech, Inc., South San Francisco, California, USA., 2003, 14, 931-942
Hernandez, P.; Müller, M. & Appel, R. D.
Automated protein identification by tandem mass spectrometry: issues and strategies.
Mass Spectrom Rev,
Swiss Institute of Bioinformatics, Geneva, Switzerland. patricia.hernandez@isb-sib.ch, 2006, 25, 235-254
Hummel, J.; Niemann, M.; Wienkoop, S.; Schulze, W.; Steinhauser, D.; Selbig, J.; Walther, D.
& Weckwerth, W.
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.
BMC Bioinformatics,
>, 2007, 8, 216
James, P.; Quadroni, M.; Carafoli, E. & Gonnet, G.
Protein identification by mass profile fingerprinting.
Biochem Biophys Res Commun,
Department of Biology, Swiss Federal Institute of Technology (E.T.H.), Zürich., 1993, 195, 58-64
178 Johnson, R. S. & Taylor, J. A.
Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry.
Mol Biotechnol, 2002, 22, 301-315
Karas, M. & Hillenkamp, F.
Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons.
Anal Chem,
1988, 60, 2299-2301
Keller, A.; Nesvizhskii, A. I.; Kolker, E. & Aebersold, R.
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Anal Chem,
2002, 74, 5383-5392
Kennedy, J. & Yi, E. C.
Use of gas-phase fractionation to increase protein identifications : application to the peroxisome.
Methods Mol Biol,
ZymoGenetics Inc., Seattle, WA, USA., 2008, 432, 217-228
King, N. L.; Deutsch, E. W.; Ranish, J. A.; Nesvizhskii, A. I.; Eddes, J. S.; Mallick, P.; Eng, J.; Desiere, F.; Flory, M.; Martin, D. B.; Kim, B.; Lee, H.; Raught, B. & Aebersold, R.
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.
Genome Biol,
Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA.
nking@systemsbiology.org, 2006, 7, R106
Kislinger, T.; Rahman, K.; Radulovic, D.; Cox, B.; Rossant, J. & Emili, A.
PRISM, a generic large scale proteomic investigation strategy for mammals.
Mol Cell Proteomics,
Program in Proteomics and Bioinformatics, Banting and Best Department of Medical
Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada., 2003, 2, 96-106 Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; King, N.; Stein, S. E. & Aebersold, R.
Development and validation of a spectral library searching method for peptide identification from MS/MS.
Proteomics, 2007, 7, 655-667
Liu, H.; Sadygov, R. G. & Yates, J. R.
A model for random sampling and estimation of relative protein abundance in shotgun proteomics.
Anal Chem,
Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA., 2004, 76, 4193-4201
Liu, J.; Bell, A. W.; Bergeron, J. J. M.; Yanofsky, C. M.; Carrillo, B.; Beaudrie, C. E. H. &
Kearney, R. E.
Methods for peptide identification by spectral comparison.
Proteome Sci, 2007, 5, 3
López-Ferrer, D.; Martínez-Bartolomé, S.; Villar, M.; Campillos, M.; Martín-Maroto, F. &
Vázquez, J.
Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.
Anal Chem,
Centro de Biología Molecular Severo Ochoa-CSIC, 28049 Cantoblanco, Madrid, Spain., 2004, 76, 6853-6860
Ma, B.; Zhang, K.; Hendrie, C.; Liang, C.; Li, M.; Doherty-Kirby, A. & Lajoie, G.
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
Rapid Commun Mass Spectrom, 2003, 17, 2337-2342
180 Mann, M.; Højrup, P. & Roepstorff, P.
Use of mass spectrometric molecular weight information to identify proteins in sequence databases.
Biol Mass Spectrom,
Department of Molecular Biology, Odense University, Denmark., 1993, 22, 338-345 Mann, M. & Wilm, M.
Error-tolerant identification of peptides in sequence databases by peptide sequence tags.
Anal Chem,
Peptide Group, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany., 1994, 66, 4390-4399
Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S. & Pandey, A.
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.
Proc Natl Acad Sci U S A, 2007, 104, 2199-2204
Mueller, L. N.; Rinner, O.; Schmidt, A.; Letarte, S.; Bodenmiller, B.; Brusniak, M.; Vitek, O.;
Aebersold, R. & Müller, M.
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.
Proteomics,
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
lukas.mueller@imsb.biol.ethz.ch, 2007, 7, 3470-3480
Nesvizhskii, A. I.
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.
J Proteomics,
Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
nesvi@umich.edu, 2010, 73, 2092-2123
Nesvizhskii, A. I. & Aebersold, R.
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
Drug Discov Today, 2004, 9, 173-181
Nilsson, T.; Mann, M.; Aebersold, R.; Yates, J. R.; Bairoch, A. & Bergeron, J. J. M.
Mass spectrometry in high-throughput proteomics: ready for the big time.
Nat Methods,
Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada. tommy.nilsson@mcgill.ca, 2010, 7, 681-685
Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.;
Resing, K. A. & Ahn, N. G.
Comparison of label-free methods for quantifying human proteins by shotgun proteomics.
Mol Cell Proteomics,
Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder 80309-0215, USA., 2005, 4, 1487-1502
Olsen, J. V.; Macek, B.; Lange, O.; Makarov, A.; Horning, S. & Mann, M.
Higher-energy C-trap dissociation for peptide modification analysis.
Nat Methods, 2007, 4, 709-712
Palagi, P. M.; Hernandez, P.; Walther, D. & Appel, R. D.
Proteome informatics I: bioinformatics tools for processing experimental data.
Proteomics,
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland.
Patricia.Palagi@isb-sib.ch, 2006, 6, 5435-5444 Pappin, D. J.; Hojrup, P. & Bleasby, A. J.
Rapid identification of proteins by peptide-mass fingerprinting.
Curr Biol,
182 Protein Sequencing Laboratory, Imperial Cancer Research Fund, PO Box 123, Lincoln's Inn Fields, London WC2A 3PX, UK., 1993, 3, 327-332
Patterson, S. D.
Data analysis--the Achilles heel of proteomics.
Nat Biotechnol,
Farmal Biomedicines, LLC, Pasadena, CA 91106, USA. scottp@farmalbiomed.com., 2003, 21, 221-222
Perkins, D. N.; Pappin, D. J.; Creasy, D. M. & Cottrell, J. S.
Probability-based protein identification by searching sequence databases using mass spectrometry data.
Electrophoresis,
Imperial Cancer Research Fund, London, UK., 1999, 20, 3551-3567
Petricoin, E. F.; Ardekani, A. M.; Hitt, B. A.; Levine, P. J.; Fusaro, V. A.; Steinberg, S. M.;
Mills, G. B.; Simone, C.; Fishman, D. A.; Kohn, E. C. & Liotta, L. A.
Use of proteomic patterns in serum to identify ovarian cancer.
Lancet,
Food and Drug Administration/National Institutes of Health Clinical Proteomics Program, Department of Therapeutic Proteins/Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA. petricoin@cber.fda.gov, 2002, 359, 572-577
Quandt, A.; Masselot, A.; Hernandez, P.; Hernandez, C.; Maffioletti, S.; Appel, R. D. &
Lisacek, F.
SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid.
Proteomics,
2009, 9, 2648-2655
Russell, S. A.; Old, W.; Resing, K. A. & Hunter, L.
Proteomic informatics.
Int Rev Neurobiol,
Center for Computational Pharmacology, University of Colorado Health Sciences Center,
Aurora, CO 80045, USA., 2004, 61, 127-157
Savitski, M. M.; Nielsen, M. L.; Kjeldsen, F. & Zubarev, R. A.
Proteomics-grade de novo sequencing approach.
J Proteome Res, 2005, 4, 2348-2354
Savitski, M. M.; Nielsen, M. L. & Zubarev, R. A.
ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.
Mol Cell Proteomics, 2006, 5, 935-948
Searle, B. C.; Dasari, S.; Turner, M.; Reddy, A. P.; Choi, D.; Wilmarth, P. A.; McCormack, A.
L.; David, L. L. & Nagalla, S. R.
High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.
Anal Chem,
2004, 76, 2220-2230
Steen, H.; Jebanathirajah, J. A.; Rush, J.; Morrice, N. & Kirschner, M. W.
Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements.
Mol Cell Proteomics,
Department of Pathology, Harvard Medical School and Children's Hospital, Boston, Massachusetts 02115, USA. hanno.steen@childrens.harvard.edu, 2006, 5, 172-181
Tanaka, K.; Waki, H.; Ido, Y.; Akita, S.; Yoshida, Y.; Yoshida, T. & Matsuo, T.
Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry
Rapid Commun. Mass Spectrom.,
Heyden & Son Limited, 1988, 2, 151-153
184 Tissot, B.; North, S. J.; Ceroni, A.; Pang, P.; Panico, M.; Rosati, F.; Capone, A.; Haslam, S.
M.; Dell, A. & Morris, H. R.
Glycoproteomics: past, present and future.
FEBS Lett,
2009, 583, 1728-1735
Ulintz, P. J.; Zhu, J.; Qin, Z. S. & Andrews, P. C.
Improved classification of mass spectrometry database search results using newer machine learning approaches.
Mol Cell Proteomics,
National Resource for Proteomics and Pathways, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA. pulintz@umich.edu, 2006, 5, 497-509
Vizcaíno, J. A.; Foster, J. M. & Martens, L.
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
J Proteomics,
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., 2010, 73, 2136-2146
White, F. M.
Quantitative phosphoproteomic analysis of signaling network dynamics.
Curr Opin Biotechnol,
Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Building 56-787a, 77 Massachusetts Avenue, Cambridge, MA 02139, United States. fwhite@mit.edu, 2008, 19, 404-409
Wu, X.; Tseng, C. & Edwards, N.
HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models.
J Comput Biol,
Department of Computer Science, University of Maryland, College Park, MD 20742, USA.,
2007, 14, 1025-1043
Wu, Z.; Lajoie, G. & Ma, B.
MSDash: mass spectrometry database and search.
Comput Syst Bioinformatics Conf,
Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B8, Canada. zwu47@csd.uwo.ca, 2008, 7, 63-71
Yates, J. R.; Speicher, S.; Griffin, P. R. & Hunkapiller, T.
Peptide mass maps: a highly informative approach to protein identification.
Anal Biochem,
Department of Molecular Biotechnology, School of Medicine, University of Washington, Seattle 98195., 1993, 214, 397-408
Zhang, W. & Chait, B. T.
ProFound: an expert system for protein identification using mass spectrometric peptide mapping information.
Anal Chem,
The Rockefeller University, New York, New York 10021, USA.
zhangw@rockvax.rockefeller.edu, 2000, 72, 2482-2489
186
Appendix
Published format
Article 1
A simple workflow to increase MS2 identification rate by subsequent spectral library search.
Erik Ahrné, Alexandre Masselot, Pierre-Alain Binz, Markus Müller, Frederique Lisacek Proteomics, 20 FEB 2009, DOI: 10.1002/pmic.200800410
Article 2
Unrestricted identification of modified proteins using MS/MS.
Erik Ahrné, Markus Müller, Frederique Lisacek
Proteomics, 22 DEC 2009 DOI: 10.1002/pmic.200900502