mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Niedermeyer, Timo H J ^a,b   Strohalm, Martin ^c  

^a UNIVERSITY OF GREIFSWALD   (Germany)

^b CYANO BIOTECH GMBH   (Germany)

^c INSTITUTE OF MICROBIOLOGY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

CRYPTOPHYCIN 1; CYCLOPEPTIDE; MICROCYSTIN LF; MICROCYSTIN LR; MICROGININ FR 1; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER PROGRAM; CYANOBACTERIUM; CYCLIC PEPTIDE TANDEM MASS SPECTRA ANNOTATION; PEPTIDE ANALYSIS; TANDEM MASS SPECTROMETRY;

COMPUTATIONAL BIOLOGY; INFORMATION STORAGE AND RETRIEVAL; PEPTIDE FRAGMENTS; PEPTIDES, CYCLIC; SOFTWARE; STATISTICS AS TOPIC; TANDEM MASS SPECTROMETRY;

CYANOBACTERIA;

EID: 84866373857     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044913     Document Type: Article

References (81)

1. Tiburzi F, Visca P, Imperi F, (2007) Do Nonribosomal Peptide Synthetases Occur in Higher Eukaryotes? IUBMB Life 59: 730-733.
2. Caboche S, Leclère V, Pupin M, Kucherov G, Jacques P, (2010) Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity. J Bacteriol 192: 5143-5150.
3. Sainis I, Fokas D, Vareli K, Tzakos AG, Kounnis V, et al. (2010) Cyanobacterial cyclopeptides as lead compounds to novel targeted cancer drugs. Mar drugs 8: 629-657.
4. Namikoshi M, Rinehart KL, (1996) Bioactive compounds produced by cyanobacteria. J Ind Microbiol Biotechnol 17: 373-384.
5. Jaspars M, Lawton LA, (1998) Cyanobacteria- a novel source of pharmaceuticals. Curr Opin Drug Discov Devel 1: 77-84.
6. Sielaff H, Christiansen G, Schwecke T, (2006) Natural products from cyanobacteria: Exploiting a new source for drug discovery. IDrugs 9: 119-127.
7. Ziemert N, Ishida K, Liaimer A, Hertweck C, Dittmann E, (2008) Ribosomal Synthesis of Tricyclic Depsipeptides in Bloom-Forming Cyanobacteria. Angew Chem Int Ed Engl 47: 7756-7759.
8. Velásquez JE, van der Donk WA, (2011) Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 15: 11-21.
9. Marahiel MA, (2009) Working outside the protein-synthesis rules: insights into non-ribosomal peptide synthesis. J Pept Sci 15: 799-807.
10. Schwarzer D, Finking R, Marahiel MA, (2003) Nonribosomal peptides: from genes to products. Nat Prod Rep 20: 275-287.
11. Strieker M, Tanović A, Marahiel MA, (2010) Nonribosomal peptide synthetases: structures and dynamics. Curr Opin Struct Biol 20: 234-240.
12. Finking R, Marahiel MA, (2004) Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 58: 453-488.
13. Tillett D, Dittmann E, Erhard M, von Döhren H, Börner T, et al. (2000) Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptide-polyketide synthetase system. Chem Biol 7: 753-764.
14. Dittmann E, Neilan BA, Börner T, (2001) Molecular biology of peptide and polyketide biosynthesis in cyanobacteria. Appl Microbiol Biotechnol 57: 467-473.
15. Christiansen G, Fastner J, Erhard M, Börner T, Dittmann E, (2003) Microcystin Biosynthesis in Planktothrix: Genes, Evolution, and Manipulation. J Bact 185: 564-572.
16. Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, et al. (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res 36: 326-331.
17. Dreyfuss M, Härri E, Hofmann H, Kobel H, Pache W, et al. (1976) Cyclosporin A and C: New Metabolites from Trichoderma polysporum. Microbiol 133: 125-133.
18. von Wartburg A, Traber R, (1988) Cyclosporins, fungal metabolites with immunosuppressive activities. Prog Med Chem 25: 1-33.
19. McCormick MH, Stark WM, Pittenger GE, Pittenger RC, McGuire JM, (1956) Vancomycin, a new antibiotic. I. Chemical and biologic properties. Antibiot Annu 3: 606-611.
20. Nagarajan R, (1991) Antibacterial Activities and Modes of Action of Vancomycin and Related Glycopeptides. Antimicrob Agents Chemother 35: 605-609.
21. Rohr J, (2006) Cryptophycin Anticancer Drugs Revisited. ACS Chem Biol 1: 747-750.
22. Wysocki VH, Resing KA, Zhang Q, Cheng G, (2005) Mass spectrometry of peptides and proteins. Methods 35: 211-222.
23. Papayannopoulos IA, (1995) The Interpretation of Collision-Induced Dissociation Tandem Mass Spectra of Peptides. Mass Spectrom Rev 14: 49-73.
24. Barlow CK, Hair RAJO, (2008) Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools. J Mass Spectrom 43: 1301-1319.
25. Harrison AG, (2009) TO b OR NOT TO b: The Ongoing Saga of Peptide b Ions. Mass Spectrom Rev 28: 640-654.
26. Paizs B, Suhai S, (2005) Fragmentation pathways of protonated peptides. Mass Spectrom Rev 24: 508-548.
27. Arnold RJ, Jayasankar N, Aggarwal D, Tang H, Radivojac P, (2006) A machine learning approach to predicting peptide fragmentation spectra. Pac Symp Biocomput 11: 219-230.
28. Frank AM, (2009) Predicting Intensity Ranks of Peptide Fragment Ions. J Proteome Res 8: 2226-2240.
29. Webb-Robertson B-JM, Cannon WR, (2007) Current trends in computational inference from mass spectrometry-based proteomics. Brief Bioinformatics 8: 304-317.
30. Li S, Arnold RJ, Tang H, Radivojac P, (2011) On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction. Anal Chem 83: 790-796.
31. Zhang Z, (2004) Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides. Anal Chem 76: 3908-3922.
32. UCSF Mass Spectrometry Facility, ProteinProspector. Available: http://prospector2.ucsf.edu/prospector/mshome.htm. (accessed September 15, 2011).
33. Masselot A (2006) InSilicoSpectro. Available: http://insilicospectro.vital-it.ch/. (accessed September 15, 2011).
34. Colinge J, Masselot A, Carbonell P, Appel RD, (2006) InSilicoSpectro: An Open-Source Proteomics Library. J Proteome Res 5: 619-624.
35. Institute for Systems Biology (ISB), Proteomics Toolkit. Available: http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html. (accessed September 15, 2011).
36. Li S (2010) PeptideART. Available: http://peptideart.sourceforge.net/. (accessed September 15, 2011).
37. 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. Anal Chem 82: 4648-4651.
38. Rusconi F, (2009) massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data. Bioinformatics 25: 2741-2742.
39. Jagannath S, Sabareesh V, (2007) Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides. Rapid Commun Mass Spectrom 21: 3033-3038.
40. Liu W-T, Ng J, Meluzzi D, Bandeira N, Gutierrez M, et al. (2009) The interpretation of tandem mass spectra obtained from cyclic non-ribosomal peptides. Anal Chem 81: 4200-4209.
41. Polfer NC, Oomens J, Suhai S, Paizs B, (2005) Spectroscopic and theoretical evidence for oxazolone ring formation in collision-induced dissociation of peptides. J Am Chem Soc 127: 17154-17155.
42. Eckart K, (1994) Mass Spectrometry of Cyclic Peptides. Mass Spectrom Rev 13: 23-55.
43. Nakamura T, Nahaki H, Kinoshita T, (1986) Amino Acid Sequence Determination of Cyclic Peptides by Tandem Mass Spectrometry Coupled with Fast Atom Bombardment Ionization. Mass Spectrosc 34: 307-319.
44. Jegorov A, Paizs B, Kuzma M, Zabka M, Landa Z, et al. (2004) Extraribosomal cyclic tetradepsipeptides beauverolides: profiling and modeling the fragmentation pathways. J Mass Spectrom 39: 949-960.
45. Schäfer M, Fuchs R, Budzikiewicz H, Springer A, Meyer J-M, et al. (2006) Structure elucidation of cyclic pyoverdins and examination of rearrangement reactions in MS/MS experiments by determination of exact product ion masses. J Mass Spectrom 41: 1162-1170.
46. Kubwabo C, Vais N, Benoit FM, (2005) Characterization of microcystins using in-source collision-induced dissociation. Rapid Commun Mass Spectrom 19: 597-604.
47. Yuan M, Namikoshi M, Otsuki A, Rinehart KL, Sivonen K, et al. (1999) Low-energy collisionally activated decomposition and structural characterization of cyclic heptapeptide microcystins by electrospray ionization mass spectrometry. J Mass Spectrom 34: 33-43.
48. Mayumi T, Kato H, Kawasaki Y, Harada K-ichi, (2007) Formation of diagnostic product ions from cyanobacterial cyclic peptides by the two-bond fission mechanism using ion trap liquid chromatography/multi-stage mass spectrometry. Rapid Commun Mass Spectrom 21: 1025-1033.
49. Eckart K, Schwarz H, Tomer KB, Gross ML, (1985) Tandem Mass Spectrometry Methodology for the Sequence Determination of Cyclic Peptides. J Am Chem Soc 107: 6765-6769.
50. Yagüe J, Paradela A, Ramos M, Ogueta S, Marina A, et al. (2003) Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra. Anal Chem 75: 1524-1535.
51. Harrison AG, Young AB, Bleiholder C, Suhai S, Paizs B, (2006) Scrambling of sequence information in collision-induced dissociation of peptides. J Am Chem Soc 128: 10364-10365.
52. Jia C, Qi W, He Z, (2007) Cyclization reaction of peptide fragment ions during multistage collisionally activated decomposition: an inducement to lose internal amino-acid residues. J Am Soc Mass Spectrom 18: 663-678.
53. Harrison AG, (2008) Peptide sequence scrambling through cyclization of b(5) ions. J Am Soc Mass Spectrom 19: 1776-1780.
54. Jia C, Qi W, He Z, (2007) Cyclization reaction of peptide fragment ions during multistage collisionally activated decomposition: an inducement to lose internal amino-acid residues. J Am Soc Mass Spectrom 18: 663-678.
55. Polfer NC, Oomens J, Suhai S, Paizs B, (2007) Infrared Spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton. J Am Chem Soc 129: 5887-5897.
56. Bythell BJ, Maître P, Paizs B, (2010) Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides. J Am Chem Soc 132: 14766-14779.
57. Fuchs R, Budzikiewicz H, (2001) Rearrangement reactions in the electrospray ionization mass spectra of pyoverdins. Int J Mass Spectrom 210-211: 603-612.
58. Bleiholder C, Osburn S, Williams TD, Suhai S, Van Stipdonk M, et al. (2008) Sequence-scrambling fragmentation pathways of protonated peptides. J Am Chem Soc 130: 17774-17789.
59. Tang XJ, Thibault P, Boyd RK, (1993) Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation. Anal Chem 65: 2824-2834.
60. Yuan M, Namikoshi M, Otsuki A, (1998) Effect of amino acid side-chain on fragmentation of cyclic peptide ions: differences of electrospray ionization/collision-induced decomposition mass spectra of toxic heptapeptide microcystins containing ADMAdda instead of Adda. Eur J Mass Spectrom 4: 287-298.
61. Schilling B, Wang W, McMurray JS, Medzihradszky KF, (1999) Fragmentation and sequencing of cyclic peptides by matrix-assisted laser desorption/ionization post-source decay mass spectrometry. Rapid Commun Mass Spectrom 13: 2174-2179.
62. Sabareesh V, Ranganayaki RS, Raghothama S, Bopanna MP, Balaram H, et al. (2007) Identification and Characterization of a Library of Microheterogeneous Cyclohexadepsipeptides from the Fungus Isaria. J Nat Prod 70: 715-729.
63. Tilvi S, Naik CG, (2007) Tandem mass spectrometry of kahalalides: identification of two new cyclic depsipeptides, kahalalide R and S from Elysia grandifolia. J Mass Spectrom 42: 70-80.
64. Tomer KB, Crow FW, Gross ML, Kopple KD, (1984) Fast atom bombardment combined with tandem mass spectrometry for the determination of cyclic peptides. Anal Chem 56: 880-886.
65. Cooper HJ, Hudgins RR, Håkansson K, Marshall AG, (2002) Characterization of amino acid side chain losses in electron capture dissociation. J Am Soc Mass Spectrom 13: 241-249.
66. Savitski MM, Nielsen ML, Zubarev RA, (2007) Side-chain losses in electron capture dissociation to improve peptide identification. Anal Chem 79: 2296-2302.
67. Xia Q, Lee MV, Rose CM, Marsh AJ, Hubler SL, et al. (2011) Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation. J Am Soc Mass Spectrom 22: 255-264.
68. Leymarie N, Costello CE, O'Connor PB, (2003) Electron Capture Dissociation Initiates a Free Radical Reaction Cascade. J Am Chem Soc 125: 8949-8958.
69. Lioe H, O'Hair RAJ, (2007) Comparison of collision-induced dissociation and electron-induced dissociation of singly protonated aromatic amino acids, cystine and related simple peptides using a hybrid linear ion trap-FT-ICR mass spectrometer. Anal Bioanal Chem 389: 1429-1437.
70. Medzihradszky KF, (2005) Peptide Sequence Analysis. Methods Enzymol 402: 209-244.
71. Deery MJ, Summerfield SG, Buzy A, Jennings KR, (1997) A Mechanism for the Loss of 60 u from Peptides Containing an Arginine Residue at the C-Terminus. J Am Soc Mass Spectrom 8: 253-261.
72. Gehrig PM, Hunziker PE, Zahariev S, Pongor S, (2004) Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS. J Am Soc Mass Spectrom 15: 142-149.
73. Bythell BJ, Csonka IP, Suhai S, Barofsky DF, Paizs B (2010) Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine. J Phys Chem B 114: 15092-15105, and references cited therein.
74. Swiderek KM, Davis MT, Lee TD, (1998) The identification of peptide modifications derived from gel-separated proteins using electrospray triple quadrupole and ion trap analyses. Electrophoresis 19: 989-997.
75. Fang S, Takao T, Satomi Y, Mo W, Ahimonishi Y (2000) Novel Rearranged Ions Observed for Protonated Peptides Via Metastable Decomposition in Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. J Am Soc Mass Spectrom 11: 345-351, and references cited therein.
76. Ngoka LCM, Gross ML, (1999) A Nomenclature System for Labeling Cyclic Peptide Fragments. Am Soc Mass Spectrom 10: 360-363.
77. Biemann K, (1992) Mass Spectrometry of Peptides and Proteins. Annu Rev Biochem 61: 977-1010.
78. Roepstorff P, Fohlman J, (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11: 601.
79. Jegorov A, Havlícek V, (2001) Spontaneous N -> O acyl shift in the [M+H]+ ions of [MeBmt1]-cyclosporins in an ion trap. J Mass Spectrom 36: 633-640.
80. Mayumi T, Kato H, Imanishi S, Kawasaki Y, Hasegawa M, et al. (2006) ORIGINAL ARTICLE Structural Characterization of Microcystins by LC/MS/MS under Ion Trap Conditions. J Antibiot 59: 710-719.
81. Namikoshi M, Rinehart KL, Sakai R, Stotts RR, Dahlem AM, et al. (1992) Identification of 12 hepatotoxins from a Homer Lake bloom of the cyanobacteria Microcystis aeruginosa, Microcystis viridis, and Microcystis wesenbergii: nine new microcystins. J Org Chem 57: 866-872.