Archive Page: Proteomic Mass Spectrometry | Scientific Resources

Archive Page: Proteomic Mass Spectrometry | Scientific Resources

Proteomic Mass Spectrometry

The Proteomic Mass Spectrometry team left the Sanger Institute in 2017. This page is being maintained as a historical record of the work of the group and is no longer being updated.
mass-spectronemy-2.jpgSanger Institute, Genome Research Limited

Our Research and Approach

Until the group left the Sanger Institute in 2017, it was interested in solving questions about the biology underlying health and disease by studying molecular processes and pathways. To do this the team used a range of techniques including mass spectrometry, biochemistry, molecular biology and informatics, to study protein function, proteome composition and organisation.

The Proteomic mass spectrometry team complemented the research programmes of the Sanger Institute to further understanding of the relationship between the genome and the proteome (entire set of expressed proteins). Through its research and collaborations the group explored protein-protein interactions, cell signalling and protein expression in a range of human, pathogen and model organisms.

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Jyoti Choudhary
Group Leader

Her research focused on the development and implementation of novel mass spectrometry approaches for proteome discovery. These methods were used to link functional information to proteins and, on a global scale, to reveal cellular network properties.

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Key Projects, Collaborations, Tools & Data

We work closely with research teams across the Sanger Institute research programmes and with many organisations around the world. If you are interested in collaborating with us please contact Jyoti Choudhary. For career opportunities with our group please visit the Sanger careers pages. We also welcome applications from self-funded post docs.

Partners and Funders

Internal Partners
External Partners and Funders


  • DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics.

    Wright JC and Choudhary JS

    Journal of proteomics & bioinformatics 2016;9;6;176-180

  • Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

    Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM et al.

    Nature communications 2016;7;11778

  • Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.

    Blohmke CJ, Darton TC, Jones C, Suarez NM, Waddington CS et al.

    The Journal of experimental medicine 2016;213;6;1061-77

  • Study of Plasmodium falciparum DHHC palmitoyl transferases identifies a role for PfDHHC9 in gametocytogenesis.

    Tay CL, Jones ML, Hodson N, Theron M, Choudhary JS and Rayner JC

    Cellular microbiology 2016;18;11;1596-1610

  • Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.

    Maggiore L, Yu L, Omasits U, Rossi O, Dougan G et al.

    International journal of medical microbiology : IJMM 2016;306;2;99-108

  • Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells.

    Bode D, Yu L, Tate P, Pardo M and Choudhary J

    Molecular & cellular proteomics : MCP 2016;15;3;878-91

  • Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

    Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E et al.

    Nucleic acids research 2016;44;D1;D746-52

  • Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage.

    Peltier J, Shaw HA, Couchman EC, Dawson LF, Yu L et al.

    The Journal of biological chemistry 2015;290;40;24453-69

  • Palmitoylation and palmitoyl-transferases in Plasmodium parasites.

    Hodson N, Invergo B, Rayner JC and Choudhary JS

    Biochemical Society transactions 2015;43;2;240-5

  • A new method to determine in vivo interactomes reveals binding of the Legionella pneumophila effector PieE to multiple rab GTPases.

    Mousnier A, Schroeder GN, Stoneham CA, So EC, Garnett JA et al.

    mBio 2014;5;4

  • p53 mediates loss of hematopoietic stem cell function and lymphopenia in Mysm1 deficiency.

    Belle JI, Langlais D, Petrov JC, Pardo M, Jones RG et al.

    Blood 2015;125;15;2344-8

  • Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.

    Kunowska N, Rotival M, Yu L, Choudhary J and Dillon N

    Nucleic acids research 2015;43;3;1418-32

  • Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.

    Collins MO, Wright JC, Jones M, Rayner JC and Choudhary JS

    Journal of proteomics 2014;103;1-14

  • The OMSSAPercolator: an automated tool to validate OMSSA results.

    Wen B, Li G, Wright JC, Du C, Feng Q et al.

    Proteomics 2014;14;9;1011-4

  • Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites.

    Brochet M, Collins MO, Smith TK, Thompson E, Sebastian S et al.

    PLoS biology 2014;12;3;e1001806

  • A polygenic burden of rare disruptive mutations in schizophrenia.

    Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N et al.

    Nature 2014;506;7487;185-90

  • Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism.

    Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP et al.

    BMC genomics 2014;15;160

  • Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes.

    Bayés À, Collins MO, Galtrey CM, Simonnet C, Roy M et al.

    Molecular brain 2014;7;88

  • Mechanisms controlling the temporal degradation of Nek2A and Kif18A by the APC/C-Cdc20 complex.

    Sedgwick GG, Hayward DG, Di Fiore B, Pardo M, Yu L et al.

    The EMBO journal 2013;32;2;303-14

  • De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

    Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M et al.

    Molecular psychiatry 2012;17;2;142-53

  • SynGAP isoforms exert opposing effects on synaptic strength.

    McMahon AC, Barnett MW, O'Leary TS, Stoney PN, Collins MO et al.

    Nature communications 2012;3;900

  • Nuclear receptor binding protein 1 regulates intestinal progenitor cell homeostasis and tumour formation.

    Wilson CH, Crombie C, van der Weyden L, Poulogiannis G, Rust AG et al.

    The EMBO journal 2012;31;11;2486-97

  • Assignment of protein interactions from affinity purification/mass spectrometry data.

    Pardo M and Choudhary JS

    Journal of proteome research 2012;11;3;1462-74

  • De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

    Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M et al.

    Molecular psychiatry 2012;17;2;142-53

  • Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins.

    Bayés A, Collins MO, Croning MD, van de Lagemaat LN, Choudhary JS and Grant SG

    PloS one 2012;7;10;e46683

  • The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

    Côté RG, Griss J, Dianes JA, Wang R, Wright JC et al.

    Molecular & cellular proteomics : MCP 2012;11;12;1682-9

  • A Plasmodium calcium-dependent protein kinase controls zygote development and transmission by translationally activating repressed mRNAs.

    Sebastian S, Brochet M, Collins MO, Schwach F, Jones ML et al.

    Cell host & microbe 2012;12;1;9-19

  • Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.

    Wright JC, Collins MO, Yu L, Käll L, Brosch M and Choudhary JS

    Molecular & cellular proteomics : MCP 2012;11;8;478-91

  • Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis.

    Jones ML, Collins MO, Goulding D, Choudhary JS and Rayner JC

    Cell host & microbe 2012;12;2;246-58

  • Coordinating cell cycle progression via cyclin specificity.

    Pagliuca FW, Collins MO and Choudhary JS

    Cell cycle (Georgetown, Tex.) 2011;10;24;4195-6

  • APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment.

    Mansfeld J, Collin P, Collins MO, Choudhary JS and Pines J

    Nature cell biology 2011;13;10;1234-43

  • Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery.

    Pagliuca FW, Collins MO, Lichawska A, Zegerman P, Choudhary JS and Pines J

    Molecular cell 2011;43;3;406-17

  • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

    Brosch M, Saunders GI, Frankish A, Collins MO, Yu L et al.

    Genome research 2011;21;5;756-67

  • Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.

    Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP et al.

    Microbiology (Reading, England) 2011;157;Pt 10;2922-2932

  • Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

    Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL et al.

    PLoS pathogens 2011;7;4;e1002018

  • Characterization of the proteome, diseases and evolution of the human postsynaptic density.

    Bayés A, van de Lagemaat LN, Collins MO, Croning MD, Whittle IR et al.

    Nature neuroscience 2011;14;1;19-21

  • Prmt5 is essential for early mouse development and acts in the cytoplasm to maintain ES cell pluripotency.

    Tee WW, Pardo M, Theunissen TW, Yu L, Choudhary JS et al.

    Genes & development 2010;24;24;2772-7

  • A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi.

    Pickard D, Toribio AL, Petty NK, van Tonder A, Yu L et al.

    Journal of bacteriology 2010;192;21;5746-54

  • An expanded Oct4 interaction network: implications for stem cell biology, development, and disease.

    Pardo M, Lang B, Yu L, Prosser H, Bradley A et al.

    Cell stem cell 2010;6;4;382-95

  • Scoring and validation of tandem MS peptide identification methods.

    Brosch M and Choudhary J

    Methods in molecular biology (Clifton, N.J.) 2010;604;43-53

  • Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.

    Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH et al.

    Molecular systems biology 2009;5;269

  • Accurate and sensitive peptide identification with Mascot Percolator.

    Brosch M, Yu L, Hubbard T and Choudhary J

    Journal of proteome research 2009;8;6;3176-81

  • A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

    Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD et al.

    PLoS genetics 2009;5;7;e1000569

  • Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores.

    Lawley TD, Croucher NJ, Yu L, Clare S, Sebaihia M et al.

    Journal of bacteriology 2009;191;17;5377-86

  • Cell biology. Evolving cell signals.

    Collins MO

    Science (New York, N.Y.) 2009;325;5948;1635-6

  • Neurotransmitters drive combinatorial multistate postsynaptic density networks.

    Coba MP, Pocklington AJ, Collins MO, Kopanitsa MV, Uren RT et al.

    Science signaling 2009;2;68;ra19

  • Mapping multiprotein complexes by affinity purification and mass spectrometry.

    Collins MO and Choudhary JS

    Current opinion in biotechnology 2008;19;4;324-30

  • Evolutionary expansion and anatomical specialization of synapse proteome complexity.

    Emes RD, Pocklington AJ, Anderson CN, Bayes A, Collins MO et al.

    Nature neuroscience 2008;11;7;799-806

  • Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.

    Brosch M, Swamy S, Hubbard T and Choudhary J

    Molecular & cellular proteomics : MCP 2008;7;5;962-70

  • Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.

    Pickard D, Thomson NR, Baker S, Wain J, Pardo M et al.

    Journal of bacteriology 2008;190;7;2580-7

  • Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder.

    Collins MO, Yu L, Campuzano I, Grant SG and Choudhary JS

    Molecular & cellular proteomics : MCP 2008;7;7;1331-48