Simon J Hubbard

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. pmc PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns
    Thomas McLaughlin
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 34:D649-54. 2006
  2. pmc Quantitative analysis of chaperone network throughput in budding yeast
    Philip Brownridge
    Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
    Proteomics 13:1276-91. 2013
  3. doi request reprint Computational approaches to peptide identification via tandem MS
    Simon J Hubbard
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
    Methods Mol Biol 604:23-42. 2010
  4. pmc Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    Andrew R Jones
    Department of Preclinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool, UK
    Proteomics 9:1220-9. 2009
  5. pmc Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins
    Andrew G Cridge
    The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
    Nucleic Acids Res 38:8039-50. 2010
  6. doi request reprint Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
    Philip Brownridge
    Protein Function Group, Institute of Integrative Biology, University of Liverpool, UK
    Proteomics 11:2957-70. 2011
  7. pmc Puf3p induces translational repression of genes linked to oxidative stress
    William Rowe
    The Faculty of Life Sciences, The Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK and Manchester Institute of Biotechnology MIB, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    Nucleic Acids Res 42:1026-41. 2014
  8. ncbi request reprint Global translational responses to oxidative stress impact upon multiple levels of protein synthesis
    Daniel Shenton
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
    J Biol Chem 281:29011-21. 2006
  9. pmc e-Fungi: a data resource for comparative analysis of fungal genomes
    Cornelia Hedeler
    School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
    BMC Genomics 8:426. 2007
  10. pmc CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches
    Claire E Eyers
    Michael Barber Centre for Mass Spectrometry, The University of Manchester, Manchester, M1 7DN, UK
    Mol Cell Proteomics 10:M110.003384. 2011

Detail Information

Publications46

  1. pmc PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns
    Thomas McLaughlin
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 34:D649-54. 2006
    ..We believe this database will be useful to proteome researchers wishing to understand gas phase peptide ion chemistry in order to improve peptide identification strategies. Questions can be addressed to j.selley@manchester.ac.uk...
  2. pmc Quantitative analysis of chaperone network throughput in budding yeast
    Philip Brownridge
    Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
    Proteomics 13:1276-91. 2013
    ..Additionally, although chaperones target fewer than 40% of annotated proteins we show that they mediate the folding of the majority of protein molecules (∼62% of the total protein flux in the cell), highlighting their importance...
  3. doi request reprint Computational approaches to peptide identification via tandem MS
    Simon J Hubbard
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
    Methods Mol Biol 604:23-42. 2010
    ..This will cover the approaches used to compare experimental and theoretical spectra and some of the methods used to validate and provide higher confidence in the assignments...
  4. pmc Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    Andrew R Jones
    Department of Preclinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool, UK
    Proteomics 9:1220-9. 2009
    ..The combined FDR Score can differentiate between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine...
  5. pmc Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins
    Andrew G Cridge
    The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
    Nucleic Acids Res 38:8039-50. 2010
    ..Thus the combined action of each 4E-BP with specific 3'-UTR-binding proteins mediates mRNA-specific translational control in yeast, showing that this form of translational control is more widely employed than previously thought...
  6. doi request reprint Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
    Philip Brownridge
    Protein Function Group, Institute of Integrative Biology, University of Liverpool, UK
    Proteomics 11:2957-70. 2011
    ..This workflow brings issues of optimal selection of quantotypic peptides, their assembly into QconCATs, expression, purification and deployment...
  7. pmc Puf3p induces translational repression of genes linked to oxidative stress
    William Rowe
    The Faculty of Life Sciences, The Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK and Manchester Institute of Biotechnology MIB, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    Nucleic Acids Res 42:1026-41. 2014
    ....
  8. ncbi request reprint Global translational responses to oxidative stress impact upon multiple levels of protein synthesis
    Daniel Shenton
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
    J Biol Chem 281:29011-21. 2006
    ..In summary, oxidative stress elicits complex translational reprogramming that is fundamental for adaptation to the stress...
  9. pmc e-Fungi: a data resource for comparative analysis of fungal genomes
    Cornelia Hedeler
    School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
    BMC Genomics 8:426. 2007
    ..Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species...
  10. pmc CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches
    Claire E Eyers
    Michael Barber Centre for Mass Spectrometry, The University of Manchester, Manchester, M1 7DN, UK
    Mol Cell Proteomics 10:M110.003384. 2011
    ..Finally, we demonstrate the improved efficacy of the general approach by applying a predictor trained on yeast data to sets of proteotypic peptides from two additional species taken from an existing peptide identification repository...
  11. pmc Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p
    Christopher J Kershaw
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
    Sci Rep 5:15518. 2015
    ....
  12. pmc Investigating protein isoforms via proteomics: a feasibility study
    Paul Blakeley
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, UK
    Proteomics 10:1127-40. 2010
    ..We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies...
  13. doi request reprint PepSeeker: mining information from proteomic data
    Jennifer A Siepen
    Faculty of Life Sciences, The University of Manchester, Manchester, UK, Michael Smith Building
    Methods Mol Biol 484:319-32. 2008
    ....
  14. pmc The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response
    Christopher J Kershaw
    Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
    PLoS Genet 11:e1004903. 2015
    ..Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control. ..
  15. pmc Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
    Craig Lawless
    Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
    BMC Genomics 10:7. 2009
    ..In particular, we highlight the potential role of 5' UTRs and upstream open reading frames (uORFs)...
  16. pmc Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor
    Emma Laing
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    BMC Genomics 9:79. 2008
    ..However, transcription factor binding sites (TFBSs), typically found upstream of the first gene in an operon, have not yet been evaluated...
  17. pmc Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
    James C Wright
    Dept Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK
    BMC Genomics 10:61. 2009
    ....
  18. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...
  19. ncbi request reprint Recent developments in proteome informatics for mass spectrometry analysis
    James C Wright
    Faculty of Life Sciences, University of Manchester, Manchester M139PT, UK
    Comb Chem High Throughput Screen 12:194-202. 2009
    ..These tools and technologies point the way towards the next phase of experimental proteomics and informatics challenges that the proteomics community will face...
  20. pmc Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring
    Craig Lawless
    From the Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
    Mol Cell Proteomics 15:1309-22. 2016
    ..This work contributes a "gold-standard" reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies. ..
  21. pmc PEDRo: a database for storing, searching and disseminating experimental proteomics data
    Kevin Garwood
    Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    BMC Genomics 5:68. 2004
    ..However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets...
  22. pmc Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    J Proteome Res 6:399-408. 2007
    ..smith.man.ac uk/MissedCleave...
  23. pmc Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies
    Paul Blakeley
    Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK
    J Proteome Res 11:5221-34. 2012
    ..These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives...
  24. pmc The mzIdentML data standard for mass spectrometry-based proteomics results
    Andrew R Jones
    Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZJ, UK
    Mol Cell Proteomics 11:M111.014381. 2012
    ....
  25. pmc FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines
    David C Wedge
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
    J Proteome Res 10:2088-94. 2011
    ....
  26. doi request reprint Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy
    Sarah R Hart
    Michael Barber Centre for Mass Spectrometry, School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
    J Am Soc Mass Spectrom 20:167-75. 2009
    ..Thus, a combined ETD/CAD approach leads to the recognition of more peptides and proteins than are achieved using peptide analysis by CAD- or ETD-based tandem mass spectrometry alone...
  27. doi request reprint Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics
    Andrew F Jarnuczak
    Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
    J Proteome Res 15:2945-59. 2016
    ..Data are available via ProteomeXchange with identifier PXD003472. ..
  28. pmc An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Proteome Sci 5:4. 2007
    ..Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed...
  29. doi request reprint An introduction to proteome bioinformatics
    Andrew R Jones
    Department of Pre clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool, UK
    Methods Mol Biol 604:1-5. 2010
    ..We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research...
  30. pmc A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis
    Faviel F Gonzalez-Galarza
    Institute of Integrative Biology, University of Liverpool, Liverpool, UK
    OMICS 16:431-42. 2012
    ..We have produced a web-based tool ( http://www.proteosuite.org/?q=other_resources ) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology...
  31. ncbi request reprint The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  32. ncbi request reprint A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    Chris F Taylor
    School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nat Biotechnol 21:247-54. 2003
    ..These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository...
  33. pmc A kingdom-specific protein domain HMM library for improved annotation of fungal genomes
    Intikhab Alam
    School of Computer Science, University of Manchester, Kilburn Building, Manchester, UK
    BMC Genomics 8:97. 2007
    ....
  34. pmc Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting
    Julie M Pratt
    Department of Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK
    Proteomics 2:157-63. 2002
    ..The method is tolerant to the extent of labelling, and as such, may be applicable to a range of single cell systems...
  35. pmc Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics
    Craig Lawless
    Faculty of Life Sciences, The University of Manchester, Manchester, UK
    OMICS 16:449-56. 2012
    ..The software has been made available at http://king.smith.man.ac.uk/mcpred ...
  36. pmc Capture and analysis of quantitative proteomic data
    King Wai Lau
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    Proteomics 7:2787-99. 2007
    ..These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge...
  37. doi request reprint Distributions of ion series in ETD and CID spectra: making a comparison
    Sarah R Hart
    Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    Methods Mol Biol 696:327-37. 2011
    ..Such data-mining efforts will prove useful in the generation of new database searching algorithms which are well suited to the analysis of ETD product ion spectra...
  38. doi request reprint Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides
    King Wai Lau
    Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
    Rapid Commun Mass Spectrom 23:1508-14. 2009
    ..We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies...
  39. pmc Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways
    Julia B Smirnova
    Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
    Mol Cell Biol 25:9340-9. 2005
    ..The transcriptional regulation of these genes has recently been connected to the regulation of cellular proliferation, and on the basis of our results, the translational control of these mRNAs should be factored into this equation...
  40. pmc Analysis of gene expression in operons of Streptomyces coelicolor
    Emma Laing
    Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK
    Genome Biol 7:R46. 2006
    ..Recent studies have shown that microarray-derived gene-expression data are useful for operon prediction. However, it is apparent that genes within an operon do not conform to the simple notion that they have equal levels of expression...
  41. pmc Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae
    Andrew F Jarnuczak
    Faculty of Life Sciences, Michael Smith Building, Manchester, UK
    Proteomics 15:3126-39. 2015
    ..This highlights how quantitative proteomics and systems modelling can be used to rationalise emergent network properties, and how the HSP70 system can accommodate the loss of major hubs. ..
  42. pmc Computational phosphoproteomics: from identification to localization
    Dave C H Lee
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    Proteomics 15:950-63. 2015
    ..Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards...
  43. pmc Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
    Simon J Hubbard
    Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom
    Genome Res 15:174-83. 2005
    ....
  44. ncbi request reprint Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics
    Patrick J Lester
    Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester, UK
    Proteomics 2:1392-405. 2002
    ..Despite this, there exists a considerable enrichment above random of tryptic peptide conservation and PMF promises to remain useful when combined with other data than just peptide masses for cross-species protein identification...
  45. ncbi request reprint Differential expression of ion channel transcripts in atrial muscle and sinoatrial node in rabbit
    James O Tellez
    University of Manchester, Manchester, M13 9NT, UK
    Circ Res 99:1384-93. 2006
    ..For example, Na(v)1.5 messenger RNA is expressed in the SAN periphery (as it is in atrial muscle), but not in the SAN center, and this is probably related to the need of the SAN periphery to drive the surrounding atrial muscle...
  46. ncbi request reprint Conservation of orientation and sequence in protein domain--domain interactions
    Stephen J Littler
    Faculty of Life Sciences, The University of Manchester, Jackson s Mill, P O Box 88, Manchester M60 1QD, UK
    J Mol Biol 345:1265-79. 2005
    ..These data suggest that there may be many more than the 2000 domain--domain interactions that have not yet been observed structurally, and we provide a top 30 hit-list of putative domain interactions which should be targeted...