Nuno Bandeira

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Protein identification by spectral networks analysis
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:6140-5. 2007
  2. ncbi request reprint Shotgun protein sequencing by tandem mass spectra assembly
    Nuno Bandeira
    Computer Science and Engineering Department, University of California, San Diego, Department 0114, 9500 Gilman Drive, La Jolla, California 92093 0114, USA
    Anal Chem 76:7221-33. 2004
  3. ncbi request reprint Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 6:1123-34. 2007
  4. pmc Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides
    Adrian Guthals
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
    J Proteome Res 12:2846-57. 2013
  5. pmc Accurate mass spectrometry based protein quantification via shared peptides
    Banu Dost
    Department of Computer Science and Engineering, UC San Diego, San Diego, California, USA
    J Comput Biol 19:337-48. 2012
  6. pmc Target-decoy approach and false discovery rate: when things may go wrong
    Nitin Gupta
    Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
    J Am Soc Mass Spectrom 22:1111-20. 2011
  7. pmc A turn-key approach for large-scale identification of complex posttranslational modifications
    Jian Wang
    Bioinformatics Program, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Computational Mass Spectrometry, and Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
    J Proteome Res 13:1190-9. 2014
  8. pmc False discovery rates in spectral identification
    Kyowon Jeong
    Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
    BMC Bioinformatics 13:S2. 2012
  9. pmc Shotgun protein sequencing with meta-contig assembly
    Adrian Guthals
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 11:1084-96. 2012
  10. pmc Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides
    Wei Ting Liu
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0636, USA
    Anal Chem 81:4200-9. 2009

Collaborators

Detail Information

Publications36

  1. pmc Protein identification by spectral networks analysis
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:6140-5. 2007
    ..In addition to speed, our approach provides a unique paradigm for identifying posttranslational modifications by means of spectral networks analysis...
  2. ncbi request reprint Shotgun protein sequencing by tandem mass spectra assembly
    Nuno Bandeira
    Computer Science and Engineering Department, University of California, San Diego, Department 0114, 9500 Gilman Drive, La Jolla, California 92093 0114, USA
    Anal Chem 76:7221-33. 2004
    ..We show that this approach not only extends the length of reconstructed amino acid sequences but also dramatically improves the quality of de novo peptide sequencing, even for low mass accuracy MS/MS data...
  3. ncbi request reprint Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 6:1123-34. 2007
    ....
  4. pmc Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides
    Adrian Guthals
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
    J Proteome Res 12:2846-57. 2013
    ..Using these strategies, we show that triplet CID/HCD/ETD MS/MS spectra from overlapping peptides yield de novo sequences of average length 70 AA and as long as 200 AA at up to 99% sequencing accuracy...
  5. pmc Accurate mass spectrometry based protein quantification via shared peptides
    Banu Dost
    Department of Computer Science and Engineering, UC San Diego, San Diego, California, USA
    J Comput Biol 19:337-48. 2012
    ..We apply our method to a model of Arabidopsis thaliana root knot nematode infection, and investigate the differential role of several protein family members in mediating host response to the pathogen...
  6. pmc Target-decoy approach and false discovery rate: when things may go wrong
    Nitin Gupta
    Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
    J Am Soc Mass Spectrom 22:1111-20. 2011
    ..Since computing FDR via TDA suffers from various restrictions, we argue that TDA is not needed when accurate p-values of individual Peptide-Spectrum Matches are available...
  7. pmc A turn-key approach for large-scale identification of complex posttranslational modifications
    Jian Wang
    Bioinformatics Program, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Computational Mass Spectrometry, and Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
    J Proteome Res 13:1190-9. 2014
    ..The core concepts of our method are readily applicable to developing algorithms for the identifications of peptides with other complex PTMs. ..
  8. pmc False discovery rates in spectral identification
    Kyowon Jeong
    Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
    BMC Bioinformatics 13:S2. 2012
    ....
  9. pmc Shotgun protein sequencing with meta-contig assembly
    Adrian Guthals
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 11:1084-96. 2012
    ..We demonstrate Meta-SPS using distinct MS/MS data sets obtained with separate enzymatic digestions and discuss how the remaining de novo sequencing limitations relate to MS/MS acquisition settings...
  10. pmc Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides
    Wei Ting Liu
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0636, USA
    Anal Chem 81:4200-9. 2009
    ....
  11. pmc Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra
    Ari M Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
    Nat Methods 8:587-91. 2011
    ..We advocate that publicly available data should be organized into spectral archives rather than be analyzed as disparate datasets, as is mostly the case today...
  12. pmc Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 8:53-69. 2009
    ..We show that such searches allow one to correct sequencing errors and find programmed frameshifts...
  13. pmc Peptide identification from mixture tandem mass spectra
    Jian Wang
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 9:1476-85. 2010
    ..Although our approach was developed for and is demonstrated on peptide spectra, we argue that the generality of the methods allows for their direct application to other types of spectral libraries and mixture spectra...
  14. pmc Spectral library generating function for assessing spectrum-spectrum match significance
    Mingxun Wang
    Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
    J Proteome Res 12:3944-51. 2013
    ....
  15. pmc Peptide identification by tandem mass spectrometry with alternate fragmentation modes
    Adrian Guthals
    Department of Computer Science and Engineering, University of California, San Diego, California, USA
    Mol Cell Proteomics 11:550-7. 2012
    ....
  16. pmc The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Cell Proteomics 9:2840-52. 2010
    ..Finally, we propose a statistical framework for analyzing multiple spectra from the same precursor (e.g. CID/ETD spectral pairs) and assigning p values to peptide-spectrum-spectrum matches...
  17. pmc Gapped spectral dictionaries and their applications for database searches of tandem mass spectra
    Kyowon Jeong
    Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA
    Mol Cell Proteomics 10:M110.002220. 2011
    ..We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches...
  18. pmc Dereplication and de novo sequencing of nonribosomal peptides
    Julio Ng
    Bioinformatics Program, University of California San Diego, La Jolla, California, USA
    Nat Methods 6:596-9. 2009
    ..We also developed an algorithm for comparative NRP dereplication that establishes similarities between newly isolated and previously identified similar but nonidentical NRPs, substantially reducing dereplication efforts...
  19. pmc MS/MS networking guided analysis of molecule and gene cluster families
    Don Duy Nguyen
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 110:E2611-20. 2013
    ..The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family-gene cluster families of hundreds or more diverse organisms in one single MS/MS network. ..
  20. pmc The spectral networks paradigm in high throughput mass spectrometry
    Adrian Guthals
    Dept Computer Science and Engineering, University of California, San Diego, USA
    Mol Biosyst 8:2535-44. 2012
    ..Here we review the current state of spectral networks algorithms and discuss possible future directions for automated interpretation of spectra from any class of molecules...
  21. pmc NeuroPedia: neuropeptide database and spectral library
    Yoona Kim
    Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California 92093 0744, USA
    Bioinformatics 27:2772-3. 2011
    ..These will also reinforce the confidence in peptide identifications by enabling visual comparisons between new and previously identified neuropeptide MS/MS spectra...
  22. pmc Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California, San Diego, USA
    Bioinformatics 24:i416-23. 2008
    ..We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry...
  23. pmc Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum
    David J Gonzalez
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
    J Biol Chem 285:28220-8. 2010
    ..is responsible for the biogenesis of a novel post-translationally modified hemolytic toxin, clostridiolysin S...
  24. pmc Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species
    Katherine R Duncan
    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
    Chem Biol 22:460-71. 2015
    ....
  25. pmc Automated genome mining of ribosomal peptide natural products
    Hosein Mohimani
    Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
    ACS Chem Biol 9:1545-51. 2014
    ..The presented tool is available at cyclo.ucsd.edu. ..
  26. pmc Peptide identification by database search of mixture tandem mass spectra
    Jian Wang
    Bioinformatics Program, University of California, San Diego, La Jolla, CA 92093, USA
    Mol Cell Proteomics 10:M111.010017. 2011
    ....
  27. pmc Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication
    Vivian Hook
    University of California, San Diego, La Jolla, 92093 0744, USA
    AAPS J 12:635-45. 2010
    ..Knowledge of the entire repertoire of neuropeptides that regulate physiological systems will provide novel insight into regulatory mechanisms in health, disease, and therapeutics...
  28. pmc Clustering millions of tandem mass spectra
    Ari M Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0404, USA
    J Proteome Res 7:113-22. 2008
    ..Our open source software MS-Clustering is available for download at http://peptide.ucsd.edu or can be run online at http://proteomics.bioprojects.org/MassSpec...
  29. ncbi request reprint Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications
    Nuno Bandeira
    University of California, San Diego, CA, USA
    Biotechniques 42:687, 689, 691 passim. 2007
    ..Open-source implementations of these algorithms may be downloaded from peptide.ucsd.edu...
  30. pmc MixGF: spectral probabilities for mixture spectra from more than one peptide
    Jian Wang
    From the Bioinformatics Program, University of California, San Diego, La Jolla, California
    Mol Cell Proteomics 13:3688-97. 2014
    ..4% of those identified in single-peptide spectra. ..
  31. pmc Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra
    Jian Wang
    Bioinformatics Program, University of California, San Diego, La Jolla, California
    Mol Cell Proteomics 13:1128-36. 2014
    ..The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. ..
  32. pmc Expanding proteome coverage with orthogonal-specificity α-lytic proteases
    Jesse G Meyer
    Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093 0378
    Mol Cell Proteomics 13:823-35. 2014
    ..The specificity of WaLP and MaLP for aliphatic amino acid side chains was particularly valuable for coverage of membrane protein sequences, which increased 350% when the data from trypsin, LysC, WaLP, and MaLP were combined. ..
  33. pmc Interkingdom metabolic transformations captured by microbial imaging mass spectrometry
    Wilna J Moree
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 109:13811-6. 2012
    ..This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations...
  34. doi request reprint Protein identification by spectral networks analysis
    Nuno Bandeira
    Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 694:151-68. 2011
    ....
  35. pmc Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 8:1391-400. 2009
    ..In addition, spectral profiles also enable intuitive visualization of all high scoring de novo reconstructions of tandem mass spectra...
  36. pmc The generating function approach for Peptide identification in spectral networks
    Adrian Guthals
    1 Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
    J Comput Biol 22:353-66. 2015
    ..After benchmarking this approach on a typical lysate MS/MS dataset, we show that the proposed intersecting spectral probabilities for spectra from overlapping peptides improve peptide identification by 30-62%. ..