Production of reliable MALDI spectra with quality threshold clustering of replicates

Journal of the American Society for Mass Spectrometry

Volumn 22, Issue 6, 2011, Pages 969-975

  Olson, Matthew T ^a   Epstein, Jonathan A ^b   Sackett, Dan L ^b   Yergey, Alfred L ^b  

^a DEPARTMENT OF PATHOLOGY   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

Consensus spectrum; MALDI; Pearson's correlation coefficient; Peptide fragmentation; QT clustering; Tubulin

Indexed keywords

CONSENSUS SPECTRUM; MALDI; PEARSON'S CORRELATION COEFFICIENTS; PEPTIDE FRAGMENTATION; QT CLUSTERING; TUBULIN;

CORRELATION METHODS; DESORPTION; MASS SPECTROMETRY; PEPTIDES;

CLUSTERING ALGORITHMS;

BETA TUBULIN; TUBULIN;

ACCURACY; AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; DNA FRAGMENTATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; QUALITY CONTROL; RAT; RELIABILITY; REPRODUCIBILITY; SPECTRAL SENSITIVITY;

AMINO ACID SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN; TUBULIN;

EID: 79955842913     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0097-9     Document Type: Article

References (41)

1. M Karas D Bachman U Bahr F Hillenkamp 1987 Matrix-assisted ultraviolet laser desorption of non-volatile compounds Int. J. Mass Spectrom. Ion Processes 78 53 68 10.1016/0168-1176(87)87041-6 1:CAS:528:DyaL2sXmsVGqsrg%3D
2. Lin, M.; Campbell, J.M.; Mueller, D.R.; Wirth, U.: Intact protein analysis by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectromety. Rapid Commun. Mass Spectrom. 17,1809-1814 (2003). (Pubitemid 36975469)
3. ZY Liu KL Schey 2005 Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis J. Am. Soc. Mass Spectrom.) 16 4 482 490 10.1016/j.jasms.2004.12.018 1:CAS:528:DC%2BD2MXisFyjtb4%3D (Pubitemid 40410034)
4. H Zhu T Yalcin L Li 1998 Analysis of the accuracy of determining average molecular weights of narrow polydispersity polymers by matrix-assosted laser desorption ionization time-of-flight mass spectrometry J. Am. Soc. Mass Spectrom. 9 275 281 10.1016/S1044-0305(97)00292-4 (Pubitemid 34436854)
5. P Chaurand F Luetzenkirchen B Spengler 1999 Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry J. Am. Soc. Mass Spectrom. 10 91 103 10.1016/S1044-0305(98)00145-7 1:CAS:528:DyaK1MXoslWmug%3D%3D (Pubitemid 34450221)
6. V Egelhofer K Büssow C Luebbert H Lehrach E Nordhoff 2000 Improvements in protein identification by MALDI-TOF-MS peptide mapping Anal. Chem. 72 13 2741 2750 10.1021/ac990686h 1:CAS:528:DC%2BD3cXjtVKnt7g%3D (Pubitemid 30452238)
7. RW Nelson D Nedelkov KA Tubbs 2000 Biosensor chip mass spectrometry: a chip-based proteomics approach Electrophoresis 21 6 1155 1163 10.1002/(SICI)1522-2683(20000401)21:6<1155::AID-ELPS1155>3.0.CO;2-X 1:CAS:528:DC%2BD3cXis12ku7s%3D (Pubitemid 30230780)
8. F Landry CR Lombardo JW Smith 2000 A method for application of samples to matrix-assisted laser desorption ionization time-of-flight targets that enhances peptide detection Anal. Biochem. 279 1 1 8 10.1006/abio.1999.4468 1:CAS:528:DC%2BD3cXht1Sgs7w%3D (Pubitemid 30148460)
9. P Berndt U Hobohm H Langen 1999 Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints Electrophoresis 20 18 3521 3526 10.1002/(SICI)1522-2683(19991201) 20:18<3521::AID-ELPS3521>3.0.CO;2-8 1:CAS:528:DC%2BD3cXhtF2nsA%3D%3D (Pubitemid 30007249)
10. K Marcus D Immler J Sternberger HE Meyer 2000 Identification of platelet proteins separated by two-dimensional gel electrophoresis and analyzed by matrix assisted laser ddesorption/ioniztion-time of flight-mass spectrometry and detection of tyrosine-phosphorylated proteins Electrophoresis 21 13 2622 2636 10.1002/1522-2683(20000701)21:13<2622::AID-ELPS2622>3.0.CO;2-3 1:CAS:528:DC%2BD3cXlsFyjs7Y%3D (Pubitemid 30646297)
11. MC Fitzgerald GR Parr LM Smith 1993 Basic matrixes for the matrix-assisted laser desorption/ionization mass spectrometry of proteins and oligonucleotides Anal. Chem. 65 22 3204 3211 10.1021/ac00070a007 1:CAS:528:DyaK3sXmt1Srur4%3D (Pubitemid 24015472)
12. Costello, C.E.; Juhasz, P.; Perreault, H.: New mass-spectral approaches to ganglioside structure determinations. In biological function of gangliosides-Proceedings of Nobel Symposium 83. In: Svennerholm, L.; Asbury, A.K.; Reisfeld, R.A.; Sandhoff, K.; Suzuki, K.; Tettamanti, G.; Toffano, G. (eds.) Progress in Brain Research, pp. 45-61. Elsevier Science Publishers B V, Amsterdam (1994)
13. P Lecchi HMT Le LK Pannell 1995 6-Aza-A-thiothymine-a matrix for MALDI spectra of oligonucleotides Nucleic Acids Res. 23 7 1276 1277 10.1093/nar/23.7.1276 1:CAS:528:DyaK2MXls1eiu78%3D
14. LA Haff P Juhasz SA Martin MT Roskey IP Smirnov EJ Takach M Vestal 1995 DNA-sequence analysis by delayed extraxction matrix-assisted laser-desorption mass-spectrometry Clin. Chem. 41 11 1680 1686
15. G Stuebiger O Belgacem 2007 Analysis of lipids using 2, 4, 6-trihydroxyacetophenone as a matrix for MALDI mass spectrometry Anal. Chem. 79 8 3206 3213 10.1021/ac062236c 1:CAS:528:DC%2BD2sXivFyqu7k%3D (Pubitemid 46640545)
16. S Jackson H Wang A Woods 2007 In situ structural characterization of glycerophospholipids and sulfatides in brain tissue using MALDI-MS/MS J. Am. Soc. Mass Spectrom. 18 1 17 26 10.1016/j.jasms.2006.08.015 1:CAS:528: DC%2BD2sXlsFCqtQ%3D%3D (Pubitemid 46038161)
17. T Mcdonald-Marsh C Carroll N Robinson A Musatov 2006 Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of cardiolipin extracted from detergent-solubilized mitochondrial electron transfer complexes Anal. Biochem. 359 2 262 264 10.1016/j.ab.2006.08.039 1:CAS:528:DC%2BD28Xht1Krtr7N (Pubitemid 44821045)
18. M Galesio R Rial-Otero J-L Capelo-Martínez 2009 Comparative study of matrices for their use in the rapid screening of anabolic steroids by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 23 12 1783 1791 10.1002/rcm.4074 1:CAS:528:DC%2BD1MXmt1ahurg%3D
19. WJ Griffiths 2003 Tandem mass spectrometry in the study of fatty acids, bile acids, and steroids Mass Spectrom. Rev. 22 2 81 152 10.1002/mas.10046 1:CAS:528:DC%2BD3sXmsV2lsrc%3D
20. WJ Griffiths S Liu G Alvelius J Sjövall 2003 Derivatization for the characterization of neutral oxosteroids by electrospray and matrix-assisted laser desorption/ionization tandem mass spectrometry: the Girard P Derivative Rapid Commun. Mass Spectrom. 17 9 924 935 10.1002/rcm.1002 1:CAS:528: DC%2BD3sXjs1OrsL4%3D (Pubitemid 36542055)
21. K Dreisewerd 2003 The desorption process in MALDI Chem. Rev. 103 395 725 10.1021/cr010375i 1:CAS:528:DC%2BD3sXlsFaruw%3D%3D
22. Karas, M.; Kruger, R.: Ion formation in MALDI: the cluster ionization mechanism. Chem. Rev. 103, 427-439 (2003)
23. R Knochenmuss R Zenobi 2003 MALDI ionization: the role of in-plume processes Chem. Rev. 103 441 452 10.1021/cr0103773 1:CAS:528: DC%2BD38XpsFCnsrc%3D
24. TW Jaskolla W-D Lehmann M Karas 2008 4-Chloro-∈∈-cyanocinnamic acid is an advanced, rationally designed MALDI matrix Proc. Natl. Acad. Sci. U. S. A. 105 34 12200 12205 10.1073/pnas.0803056105 1:CAS:528:DC%2BD1cXhtVOhtr3I
25. P Juhasz CE Costello K Biemann 1993 Matrix-assisted laser desorption ionization mass-spectrometry with 2-(4-hydroxypheny(azo)benzoic acid matrix J. Am. Soc. Mass Spectrom. 4 5 399 409 10.1016/1044-0305(93)85005-I 1:CAS:528:DyaK2cXivFehur0%3D
26. P Lorkiewicz MC Yappert 2009 2-(2-Aminoethylamino)-5-nitropyridine as a basic matrix for negative-mode matrix-assisted laser desorption/ionization analysis of phospholipids J. Mass Spectrom. 44 1 137 143 10.1002/jms.1483 1:CAS:528:DC%2BD1MXhs1Kktbs%3D
27. S Mirza N Prasada Raju S Madhavendra 2004 5-amino-2-mercapto-1, 3, 4-thiadiazole: a new matrix for the efficient matrix-assisted laser desorption/ionization of neutral carbohydrates Rapid Commun. Mass Spectrom. 18 1666 1674 10.1002/rcm.1536 1:CAS:528:DC%2BD2cXlvFegsbw%3D (Pubitemid 38937383)
28. IP Smirnov X Zhu T Taylor Y Huang P Ross IA Papayanopoulos SA Martin DJ Pappin 2004 Suppression of∈∈-cyano-4-hydroxycinnamic acid matrix clusters and reduction of chemical noise in MALDI-TOF mass spectrometry Anal. Chem. 76 10 2958 2965 10.1021/ac035331j 1:CAS:528:DC%2BD2cXivFKqt74%3D (Pubitemid 38657725)
29. DW Armstrong LK Zhang LF He ML Gross 2001 Ionic liquids as matrixes for matrix-assisted laser desorption/ionization mass spectrometry Anal. Chem. 73 15 3679 3686 10.1021/ac010259f 1:CAS:528:DC%2BD3MXksFemu74%3D (Pubitemid 32867301)
30. YL Li ML Gross 2004 Ionic-liquid matrices for quantitative analysis by MALDI-TOF mass spectrometry J. Am. Soc. Mass Spectrom. 15 12 1833 1837 10.1016/j.jasms.2004.08.011 1:CAS:528:DC%2BD2cXhtVKksLzM (Pubitemid 39602733)
31. MT Olson Blank PS DL Sackett AL Yergey 2008 Evaluating reproducibility and similarity of mass and intensity data in complex spectra-applications to tubulin J. Am. Soc. Mass Spectrom. 19 3 367 374 10.1016/j.jasms.2007.11.012 1:CAS:528:DC%2BD1cXjtlWjsrk%3D
32. Mcdonnell, L.A.; Van Remoortere, A.; van Zeijl, R.J.M.; Deelder, A.M.: Mass spectrometry image correlation: quantifying colocalization. J. Proteome Res. 7(8), 3619-3627 (2008)
33. W Jiang Y Qiu Y Ni M Su W Jia X Du 2010 An automated data analysis pipeline for GC-TOF-MS metabonomics studies J. Proteome Res. 9 11 5974 5981 10.1021/pr1007703 1:CAS:528:DC%2BC3cXht1ahtbjI
34. LJ Heyer S Kruglyak S Yooseph 1999 Exploring expression data: identification and analysis of coexpressed genes Genome Res. 9 11 1106 1115 10.1101/gr.9.11.1106 1:CAS:528:DyaK1MXns12ktrc%3D
35. A Frank N Bandeira Z Shen S Tanner S Briggs R Smith PA Pevzner 2008 Clustering millions of tandem mass spectra J. Proteome Res. 7 113 122 10.1021/pr070361e 1:CAS:528:DC%2BD2sXhsVWgur%2FN (Pubitemid 351171122)
36. Gjukich, M. 2007 T2Extractor. In https://proteomecommons.org/linktracker. jsp?url=http%3A%2F%2Fwww.proteomecommons.org%2Farchive%2F1114637208624%2F. P.C. Administrator, ed: Proteome Comons, Univ. Michigan.
37. J Wolff DL Sackett L Knipling 1996 Cation selective promotion of tubulin polymerization by alkali metal chlorides Protein Sci. 5 10 2020 2028 10.1002/pro.5560051008 1:CAS:528:DyaK28Xmt1CntL8%3D (Pubitemid 26347737)
38. DL Sackett L Knipling J Wolff 1991 Isolation of microtubule protein from mammalian brain frozen for extended periods of time Protein Expr. Purif. 2 5/6 390 393 10.1016/1046-5928(91)90099-5 1:CAS:528:DyaK38XlsV2ksw%3D%3D
39. DL Sackett 1995 Rapid purification of tubulin from tissue and tissue culture cells using solid-phase ion exchange Anal. Biochem. 228 2 343 348 10.1006/abio.1995.1361 1:CAS:528:DyaK2MXntFWqsro%3D
40. AS Woods AY Huang RJ Cotter GR Pasternack DM Pardoll EM Jaffee 1995 Simplified high-sensitivity sequencing of a major histocompatibility complex class I-associated immunoreactive peptide using matrix-assisted laser desorption/ionization mass spectrometry Anal. Biochem. 226 1 15 25 10.1006/abio.1995.1185 1:CAS:528:DyaK2MXks1Cktrc%3D
41. MT Olson JA Epstein AL Yergey 2006 De novo peptide sequencing using exhaustive enumeration of peptide composition J. Am. Soc. Mass Spectrom. 17 8 1041 1049 10.1016/j.jasms.2006.03.007 1:CAS:528:DC%2BD28XnsFOks74%3D (Pubitemid 44094120)