Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Aitken A (1990): Identification of Protein Consensus Sequences. Chichester, UK: Ellis Horwood
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990): Basic local alignment search tool. J Mol Biol 215:403–410
Bairoch A (1997): Proteome databases. In: Proteome Research: New Frontiers in Functional Genomics, Wilkins MR, Williams KL, Appel RD, Hochstrasser DF, eds. Berlin: Springer-Verlag
Bairoch A, Apweiler R (1997): The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res 25:31–36
Bairoch A, Bucher P, Hofmann K (1997): The PROSITE database, its status in 1997. Nucleic Acids Res 25:217–221
Barrett AJ et al ed. (1998): Handbook of Proteolytic Enzymes CD-ROM. San Diego, CA: Academic Press
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonhammer EL (2000): The Pfam protein families database. Nucleic Acids Res 30:276–280
Beavis RC, Fenyo D (2000): In: Proteomics: A Trends Guide, Mann M, Blackenstock W, eds. London: Elsevier, pp. 12–17
Bergman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000): The protein data bank. Nucleic Acids Rec 28:235–242
Bergman T (2000): Ladder sequencing. Experientia Supplementa 88:133–144
Berndt P, Hobohm U, Langen H (1999): Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20:3521–3526
Boyle WJ, Van der Geer P, Hunter T (1991): Phosphopeptide mapping and phosphoamino acid analysis by two-dimensional separation on thin-layer cellulose plates. Methods Enzymol 201:110–111
Cedano J, Aloy P, Perez-Pons JA, Querol E (1997): Relation between amino acid composition and cellular location of proteins. J Mol Biol 266:594–600
Celis JE, Rasmussen HH, Leffers H, Madsen P, Honore B, Gesser B, Dejgaard K, Vandekerckhove J (1991): Human cellular protein patterns and their link to genome DNA sequence data: Usefulness of two-dimensional gel electrophoresis and microsequencing. FASEB J 5:2200–2208
Choli T, Kapp U, Wittmann-Liebold B (1989): Blotting of proteins onto immobilon membranes: In situ characterization and comparison with high performance liquid chromatography. J Chromatogr 476:59–72
Cleveland DW, Fischer SG, Kirschner MW, Laemmli UK (1977): Peptide mapping by limited proteolysis in SDS by gel electrophoresis. J Biol Chem 252:1102–1106
Cohen SL, Chait BT (1997): Mass spectrometry of whole proteins eluted from SDS-PAGE gels. Anal Biochem 247:257–267
Cottrell JS, Sutton CW (1996): The identification of electrophoretically separated proteins by peptide mass fingerprinting. In: Methods in Molecular Biology Vol. 61: Protein and Peptide Analysis by Mass Spectrometry, Chapman JR, ed. Totowa, NJ: Humana Press Inc.
Courchesne PL, Patterson SD (1999): Identification of proteins by matrix-assisted laser desorption/ionization mass spectrometry using peptide and fragment ion masses. Methods Mol Biol 112:487–511
Creasy DM, Cottrell, JS (2002): Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2:1426–1434
Crimmins DL, McCourt DW, Thoma TS, Scott MG, Macke K, Schwartz BD (1990): In situ chemical cleavage of proteins immobilized to glass-fiber and polyvinylidenedifluoride membranes: Cleavage at tryptophan residues with 2-(2′-nitrophenylsulfenyl)-3-methyl-3′-bromoindolenine to obtain internal amino acid sequence. Anal Biochem 187:27–38
Dayhoff MO, Eck RV (1966): Atlas of Protein Sequence and Structure. Silver Spring, MD: National Biomedical Research Foundation
Degani Y, Patchornik A (1971): Selective cyanylation of sulfhydryl groups. II. On the synthesis of 2-Nitro-5-thiocyanatobenzoic acid. J Org Chem 36:2727
Deshpande KL, Fried VA, Ando M, Webster G (1987): Glycosylation affects cleavage of an H5N2 influenza virus hemagglutinin and regulates virulence. Proc Natl Acad Sci USA 84:36–40
Doolittle RF, Hunkapiller MW, Hood LE, Devare SG, Robbins KC, Aaronson SA, Antoniades HN (1983): Simian sarcoma virus oncgene, r-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor. Science 221:275–276
Downs F, Peterson C, Murty VLN, Pigman W (1977): Quantitation of the beta-elimination reaction as used on glycoproteins. Int J Peptide Protein Res 10:315–322
Edman P, Begg G (1967): A protein sequenator. Eur J Biochem 1:80–91
Eng J, McCormack AL, Yates JR III (1994): J Am Soc Mass Spectrom 5:976–989
Evans RW, Aitken A, Patel KJ (1988): Evidence for a single glycan moiety in rabbit serum transferrin and location of the glycan within the polypeptide chain. FEBS Lett 238:39–42
Fenyö D (2000): Identifying the proteome: software tools. Curr Opin Biotechnol 11:391–395
Fenyö D, Qin J, Chait BT (1998): Protein identification using mass spectrometric information. Electrophoresis 19:998–1005
Fernandez J, DeMott M, Atherton D, Mische SM (1992): Internal protein sequence analysis: enzymatic digestion for less than 10 micrograms of protein bound to polyvinylidene difluoride or nitrocellulose membranes. Anal Biochem 201:255–264
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999): Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999
Hearn MTW, Aguilar MI (1988): Reversed phase high performance liquid chromatography of peptides and proteins. In: Modern Physical Methods in Biochemistry, Neuberger A, Van Deenen LLM, eds. Amsterdam: Elsevier
Henikoff JG, Greene EA, Pietrokovski S, Henikoff S (2000): Increased coverage of protein families with the blocks database servers. Nucleic Acids Res 28:228–230
Hochstrasser DF, Patchornik A, Merril CR (1988): Development of polyacrylamide gels that improve the separation of proteins and their detection by silver staining. Anal Biochem 173:412–423
Hulmes JD, Miedel MC, Pan Y CE (1989): Strategies for microcharacterization of proteins using direct chemistry on sequencer supports. In: Techniques in Protein Chemistry, Hugh TE, ed. San Diego: Academic Press
Ibba M (2002): Biochemistry and bioinformatics: when worlds collide. Trends Biochem Sci 27:64
James P, Quadroni M, Carafoli E, Gonnet G (1994): Protein identification in DNA databases by peptide mass fingerprinting. Protein Sci 3: 1347–1350
Jeno P, Mini T, Moes S, Hintermann E, Horst M (1995): Internal sequences from proteins digested in polyacrylamide gels. Anal Biochem 224:75–82
Inglis AS (1983): Cleavage at aspartic acid. Methods Enzymol 91:324–332
Keil B, Tong NT (1988): Database lysis: computer-assisted investigation of cleavage sites in proteins. In: Methods in Protein Sequence Analysis, Wittman-Liebold B, ed. Heidelberg: Springer-Verlag
Kilic F, Ball EH (1991): Partial cleavage mapping of the cytoskeletal protein vinculin. J Biol Chem 266:8734–8740
Kostka V, Carpenter FH (1964): Inhibition of chymotrypsin activity in crystalline trypsin preparations. J Biol Chem 239:1799–1803
Lin J-H, Wu X-R, Kreibich G, Sun T-T (1994): Precursor sequence, processing and urothelium-specific expression of a major 15-kDa protein subunit of asymmetric unit membrane. J Biol Chem 269:1775–1784
Lipman DJ, Pearson WR (1985): Rapid and sensitive protein similarity searches. Science 227:1435–1441
Lischwe MA, Sung MA (1977): Use of N-chlorosuccinimide/urea for the selective cleavage of tryptophanyl peptide bonds in proteins. J Biol Chem 252:4976–4980
Loo RR, Dales N, Andrews PC (1994): Surfactant effects on protein structure examined by electrospray ionization mass spectrometry. Protein Sci 3:1975–1983
Lui M, Tempst P, Erdjument-Bromage H (1996): Methodical analysis of protein-nitrocellulose interactions to design a refined digestion protocol. Anal Biochem 241:156–166
Mann M, Hendrickson RC, Pandey A (2001): Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70:437–473
Mann M, Hojrup P, Roepstoff P (1993): Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 22:338–345
Mann M, Jensen ON (2003): Proteomic analysis of post-translational modifications. Nature Biotechnol 21:255–261
Mann M, Ong S-E, Gronborg M, Steen H, Jensen ON, Pandey A (2002): Analysis of protein phosphorylation using mass spectreometry: deciphering the phosphoproteome. TRENDS Biotechnol 20:261–268
Mann M, Pandey A (2001): Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. TRENDS Bio Sci 26:54–61
Mann M, Wilm M (1994): Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66:4390–4399
Martz E (2002): Protein Explorer: easy yet powerful macromolecular visualization. TRENDS Bio Sci 27:107–109
Miczka G, Kula MR (1989): The use of polyvinylidene difluoride membranes as blotting matrix in combination with sequencing; applications to pyruvate decarboxylase from Zymomonas mobilis. Anal Lett 22:2771–2782
Morris HR, Paxton T, Dell A, Langhorne J, Bordoli RS, Hoyes J, Bateman RH (1996): High sensitivity collisionally activated decomposition tandem mass spectrometry on a novel quadrapole/orthogonal-acceleration Time-of-Flight mass spectrometer. Rapid Commun Mass Spectrom 10:889–896
Moore S, Stein WH (1963): Chromatographic determination of amino acids by the use of automatic recording equipment. Methods Enzymol 6:819–831
Moos M, Nguyen NY, Liu T-Y (1988): Reproducible, high yield sequencing of proteins electrophoretically separated and transferred to an inert support. J Biol Chem 263:6005–6008
Nadler T, Parker K, Huang Y, Degnore J, Wolf B, Anderson L, Anderson N, Lennon J, Bappanad D, McGrath A (2000): Automation of gel slice extraction and MALDI-TOF-MS sample preparation on a robotic platform. in: Proceedings of the 48th ASMS Conference on Mass Spectrometry and Allied Topics. Long Beach, CA, pp. 345–346
Nefsky B, Bretscher A (1989): Landmark mapping: a general method for localizing cysteine residues within a protein. Proc Natl Acad Sci USA 86:3549–3553
Pandey A, Mann M (2000): Proteomics to study genes and genomes. Nature 405:837–846
Pappin DJC, Hojrup P, Bleasby AJ (1993): Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3:327–332
Park Z-Y, Russell DH (2000): Thermal denaturation: a useful technique in peptide mass mapping. Anal Chem 72:2667–2670
Park Z-Y, Russell DH (2001): Identification of individual proteins in complex protein mixtures by high-resolution, high-mass-accuracy MALDI TOF-mass spectrometry analysis of in-solution thermal denaturation/enzymatic digestion. Anal Chem 73:2558–2564
Patterson SD, Aebersold R (1995): Mass spectrometric approaches for the identification of gel-separated proteins. Electrophoesis 16:1791–1814
Perkins DN, Pappin DJ, Creasey DM, Cottrell (1999): Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567
Rappsilber J, Mann M (2002): What does it mean to identify a protein in proteomics? TRENDS Biochem Sci 27:74–78
Rasmussen HH, Van Damme J, Bauw G, Puype M, Gesser B, Celis JE, Vandekerckhove J (1991): Protein electroblotting and microsequencing in establishing integrated human protein databases. In: Methods in Protein Sequence Analysis, Jörnvall H, Höög JO, eds. Basel: Birkhäuser Verlag
Saris CJM, van Eenbergen J, Jenks BG, Bloemers HPJ (1983): Hydroxylamine cleavage of proteins in polyacrylamide gels. Anal Biochem 132:54–67
Scott MG, Crimmins DL, McCourt DW, Tarrand JJ, Eyerman MC, Nahm, MH (1988): A simple in situ cyanogen bromide cleavage method to obtain internal amino acid sequence of proteins electroblotted to polyvinyldifluoride membranes. Biochem Biophys Res Commun 155:1353–1359
Shevchenko A, Loboda A, Shevchenko A, Ens W, Standing KG (2000): MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal Chem 72:2132–2141
Shevchenko A, Wilm M, Vorm O, Mann M (1996): Anal Chem 68:850–858
Shultz J et al (2002): SMART: A web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28:231–234
Spahr CS, Susin SA, Bures EJ, Robinson JH, Davis MT, McGinley MD, Kroemer G, Patterson SD (2000): Simplification of complex peptide mixtures for proteomic analysis: reversible biotinylation of cysteinyl peptides. Electrophoresis 21:1635–1650
Spengler B (2001): The basics of Matrix-assisted laser desorption, ionization time-of-flight mass spectrometry and post-source decay analysis. In: Proteome Research: Mass Spectrometry Principles and Practice, James P, ed. Berlin: Springer-Verlag
Stone KL, LoPresti MB, Crawford JM, DeAngelis R, Williams KR (1989): Reverse phase HPLC separation of sub-nanomole amounts of peptides obtained from enzymatic digests. In: HPLC of Peptides and Proteins: Separation, Analysis and Conformation, Hodges RS, ed. Boca Raton, FL: CRC Press
Tabb DL, Eng JK, Yates JR III (2001): Protein identification by SEQUEST. In: Proteome Research: Mass Spectrometry, James P, ed. Berlin: Springer-Verlag
Tabb DL, McDonald WH, Yates JR (2002): DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1:21–26
Vanfleteren JR, Raymackers JG, Van Bun SM, Meheus LA (1992): Peptide mapping and microsequencing of proteins separated by SDS-PAGE after limited in situ acid hydrolysis. BioTechniques 12:551–557
Van Montfort BA, Canas B, Duurkens R, Godavac-Zimmermann, Robillard GT (2002): Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mass Spectrometry 37:322–330
Valaskovic GA, Kelleher NL, McLafferty FW (1996): Attomole protein characterization by capillary electrophoresis-mass spectrometry. Science 273:1199–1202
Vorburger K, Kitten GT, Nigg EA (1989): Modification of nuclear lamin proteins by a mevalonic acid derivative occurs in reticulocyte lysates and requires the cysteine residue of the C-terminal CXXM motif. EMBO J 8:4007–4013
Waterman MS, Vingron M (1994): Rapid and accurate estimates of statistical significance for sequence data base searches. Proc Natl Acad Sci USA 91:4625–4628
Weber K, Osborn M (1975): Proteins and sodium dodecyl sulfate: Molecular weight determination on polyacrylamide gels and related procedures. In: The Proteins, Vol. I, Neurath H, Hill RL, eds. New York: Academic Press
Wilbur WJ, Lipman DJ (1983): Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci USA 80:726–730
Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, Sanchez J-C, Yan JX, Gooley AA, Hughes G, Humphery-Smith I, Williams KL, Hochstrasser DF (1996): From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14:61–65
Wilkins MR, Gasteiger E, Bairoch A, Sanchez J-C, Williams KL, Appel RD, Hochstrasser DF (1998): Protein identification and analysis tools in the ExPASy server. In: 2-D Proteome Analysis Protocols, AJ Link, ed. New Jersey: Humana Press
Wilkins MR, Gasteiger E, Bairoch A, Sanchez J-C, Williams KL, Appel, RD, Hochstrasser DF (1999): Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 112:531–552
Wilm M, Mann M (1996): Analytical properties of the nanoelectrospray ion source. Anal Chem 68:1–8
Wilson JF (2002): The rise of biological databases. The Scientist Mar 18 p. 34–35
Zhang W, Chait BT (2000): ProFound-an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 72:2482–24
Rights and permissions
Copyright information
© 2005 Birkhäuser Boston
About this chapter
Cite this chapter
(2005). Identification of the Target Protein. In: Protein Analysis and Purification. Birkhäuser Boston. https://doi.org/10.1007/0-8176-4412-1_8
Download citation
DOI: https://doi.org/10.1007/0-8176-4412-1_8
Publisher Name: Birkhäuser Boston
Print ISBN: 978-0-8176-4340-9
Online ISBN: 978-0-8176-4412-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)