Accelerated identification of proteins by mass spectrometry by employing covalent pre-gel staining with Uniblue A

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Mata Gómez, Marco A ^a   Yasui, Matthew T ^b   Guerrero Rangel, Armando ^c   Valdés Rodríguez, Silvia ^c   Winkler, Robert ^a,c  

^a SCHOOL OF ENGINEERING AND SCIENCES   (Mexico)

^b Oregon State University   (United States)

^c DEPARTAMENTO DE INGENIERÍA GENÉTICA   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

DYE; UNCLASSIFIED DRUG; UNIBLUE A; AMINO ACID; ANAZOLENE SODIUM; ANTHRAQUINONE DERIVATIVE; ESCHERICHIA COLI PROTEIN; FUCHSINE; PEPTIDE; PROTEIN; SULFONIC ACID DERIVATIVE;

ACCURACY; ARTICLE; CHEMICAL STRUCTURE; CONTROLLED STUDY; COVALENT BOND; DERIVATIZATION; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; NUCLEOPHILICITY; PREDICTION; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN ELECTROPHORESIS; PROTEIN MODIFICATION; PROTEOMICS; SENSITIVITY AND SPECIFICITY; STAINING; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS; VALIDATION PROCESS; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; ESCHERICHIA COLI; GEL; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN DATABASE; STANDARD;

AMINO ACID SEQUENCE; AMINO ACIDS; ANTHRAQUINONES; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GELS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEINS; REFERENCE STANDARDS; ROSANILINE DYES; STAINING AND LABELING; SULFONIC ACIDS;

EID: 84857160431     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031438     Document Type: Article

References (43)

1. Rathore A, (2009) Roadmap for implementation of quality by design (QbD) for biotechnology products. Trends in Biotechnology 27: 546-553.
2. Lewis K, (2009) China's counterfeit medicine trade booming. CMAJ: Canadian Medical Association journal = journal de l'Association medicale canadienne 181.
3. Akunyili D, (2008) Fake drugs: lessons for the world. Dora Akunyili interviewed by Meredith Wadman. Nature 452.
4. Lancet, (2011) Fighting fake drugs: the role of WHO and pharma. Lancet 377.
5. Rabilloud T, (2002) Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2: 3-10.
6. Laemmli UK, (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
7. Winkler R, García-Lara S, (2010) Activity-directed identification of maize kernel peroxidases associated with postharvest insect resistance. Mol Biosyst 6: 1810-1812.
8. Gharahdaghi F, Weinberg C, Meagher D, Imai B, Mische S, (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20: 601-605.
9. Sumpton D, Bienvenut W, (2009) Coomassie stains: are they really mass spectrometry compatible? Rapid communications in mass spectrometry: RCM 23: 1525-1529.
10. Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, et al. (2004) Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 25: 1327-1333.
11. Westermeier R, (2006) Sensitive, quantitative, and fast modifications for Coomassie Blue staining of polyacrylamide gels. Proteomics 6 (Suppl 2): 61-64.
12. Jenö P, Mini T, Moes S, Hintermann E, Horst M, (1995) Internal Sequences from Proteins Digested in Polyacrylamide Gels. Analytical Biochemistry 224: 75-82.
13. Rosenfeld J, Capdevielle J, Guillemot J, Ferrara P, (1992) In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Analytical Biochemistry 203: 173-179.
14. Shevchenko A, Wilm M, Vorm O, Mann M, (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Analytical chemistry 68: 850-858.
15. Shevchenko A, Tomas H, Havlis J, Olsen J, Mann M, (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1: 2856-2860.
16. Bradford MM, (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72: 248-254.
17. Parkinson D, Redshaw J, (1984) Visible labeling of proteins for polyacrylamide gel electrophoresis with dabsyl chloride. Analytical Biochemistry 141: 121-126.
18. Compton M, Lapp S, Pedemonte R, (2002) Generation of multicolored, prestained molecular weight markers for gel electrophoresis. Electrophoresis 23: 3262-3265.
19. Usaite R, Wohlschlegel J, Venable J, Park S, Nielsen J, et al. (2008) Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The Comparison of Two Quantitative Methods. J Proteome Res 7: 266-275.
20. Elias J, Gygi S, (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature methods 4: 207-214.
21. Geer L, Markey S, Kowalak J, Wagner L, Xu M, et al. (2004) Open Mass Spectrometry Search Algorithm. Journal of Proteome Research 3: 958-964.
22. Keller A, Nesvizhskii A, Kolker E, Aebersold R, (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Analytical chemistry 74: 5383-5392.
23. Nesvizhskii A, Keller A, Kolker E, Aebersold R, (2003) A statistical model for identifying proteins by tandem mass spectrometry. Analytical chemistry 75: 4646-4658.
24. Vizcaíno JA, Côté R, Reisinger F, Foster J, Mueller M, et al. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9: 4276-4283.
25. Barsnes H, Vizcaino J, Eidhammer I, Martens L, (2009) PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology 27: 598-599.
26. Perona J, Craik C, (1995) Structural basis of substrate specificity in the serine proteases. Protein Science 4: 337-360.
27. Rice R, (1977) Stabilization of bovine trypsin by reductive methylation. Biochimica et Biophysica Acta (BBA)- Protein Structure 492: 316-321.
28. Labouesse J, Gervais M, (1967) Preparation of Chemically Defined εN-Acetylated Trypsin. European Journal of Biochemistry 2: 215-223.
29. Winkler R, (2010) ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data. Rapid communications in mass spectrometry: RCM 24: 285-294.
30. Smith M, (2003) Rituximab (monoclonal anti-CD20 antibody): mechanisms of action and resistance. Oncogene 22: 7359-7368.
31. Keough T, Youngquist RS, Lacey MP, (1999) A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry. Proceedings of the National Academy of Sciences 96: 7131-7136.
32. Bauer M, Sun Y, Keough T, Lacey M, (2000) Sequencing of sulfonic acid derivatized peptides by electrospray mass spectrometry. Rapid Commun Mass Spectrom 14: 924-929.
33. Garcia B, Mollah S, Ueberheide B, Busby S, Muratore T, et al. (2007) Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protocols 2: 933-938.
34. Valdes-Rodriguez S, Cedro-Tanda A, Aguilar-Hernandez V, Cortes-Onofre E, Blanco-Labra A, et al. (2010) Recombinant amaranth cystatin (AhCPI) inhibits the growth of phytopathogenic fungi. Plant physiology and biochemistry: PPB/Société française de physiologie végétale 48: 469-475.
35. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, et al. (2005) Protein Identification and Analysis Tools on the ExPASy Server. In: Walker JM, editors. The proteomics protocols handbook pp. 571-607.
36. Sambrook J, Russell D, Sambrook J, (2001) Molecular cloning: a laboratory manual (3-volume set). Cold Spring Harbor Laboratory Press.
37. Bjellqvist B, Ek K, Righetti P, Gianazza E, Görg A, et al. (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. Journal of biochemical and biophysical methods 6: 317-339.
38. Shevchenko A, Tomas H, Havlis J, Olsen J, Mann M, (2007) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature Protocols 1: 2856-2860.
39. Havlis J, Thomas H, Sebela M, Shevchenko A, (2003) Fast-response proteomics by accelerated in-gel digestion of proteins. Analytical chemistry 75: 1300-1306.
40. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic acids research 36: D901-906.
41. Keller A, Eng J, Zhang N, Li X, Aebersold R, (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Molecular Systems Biology 1: msb4100024-E1-msb4100024-E8.
42. Strohalm M, Kavan D, Novák P, Volný M, Havlícek V, (2010) mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. Analytical Chemistry 82: 4648-4651.
43. Chen H, Boutros P, (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12: 35.