Kathryn S Lilley

Kathryn S Lilley

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Kathryn S Lilley

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Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules.

J Proteome Res 2019 Jun 22;18(6):2525-2534. Epub 2019 May 22.

Cambridge Centre for Proteomics, Department of Biochemistry , University of Cambridge , Cambridge CB2 1QR , U.K.

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http://dx.doi.org/10.1021/acs.jproteome.9b00076DOI Listing
June 2019

Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms.

BMC Plant Biol 2019 Apr 11;19(1):139. Epub 2019 Apr 11.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.

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https://bmcplantbiol.biomedcentral.com/articles/10.1186/s128
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http://dx.doi.org/10.1186/s12870-019-1750-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460520PMC
April 2019

A Bioconductor workflow for the Bayesian analysis of spatial proteomics.

F1000Res 2019 11;8:446. Epub 2019 Apr 11.

Université catholique de Louvain, Brussels, 1200, Belgium.

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http://dx.doi.org/10.12688/f1000research.18636.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509962PMC
April 2019

Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae.

FEMS Yeast Res 2019 03;19(2)

Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.

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http://dx.doi.org/10.1093/femsyr/foz014DOI Listing
March 2019

A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells.

Sci Rep 2019 Mar 1;9(1):3270. Epub 2019 Mar 1.

Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa.

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http://dx.doi.org/10.1038/s41598-019-39400-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397265PMC
March 2019

The subcellular organisation of Saccharomyces cerevisiae.

Curr Opin Chem Biol 2019 02 29;48:86-95. Epub 2018 Nov 29.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13675931183013
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http://dx.doi.org/10.1016/j.cbpa.2018.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391909PMC
February 2019

Assessing sub-cellular resolution in spatial proteomics experiments.

Curr Opin Chem Biol 2019 02 14;48:123-149. Epub 2018 Dec 14.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.

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http://dx.doi.org/10.1016/j.cbpa.2018.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391913PMC
February 2019

Editorial overview: Untangling proteome organization in space and time.

Curr Opin Chem Biol 2019 02;48:A1-A4

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cbpa.2019.02.001DOI Listing
February 2019

Proteomic responses of HepG2 cell monolayers and 3D spheroids to selected hepatotoxins.

Toxicol Lett 2019 Jan 28;300:40-50. Epub 2018 Oct 28.

Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03784274183181
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http://dx.doi.org/10.1016/j.toxlet.2018.10.030DOI Listing
January 2019

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics.

Nat Commun 2019 01 18;10(1):331. Epub 2019 Jan 18.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.

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http://dx.doi.org/10.1038/s41467-018-08191-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338729PMC
January 2019

Identification of the RNA polymerase I-RNA interactome.

Nucleic Acids Res 2018 11;46(20):11002-11013

Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237751PMC
November 2018

A Bayesian mixture modelling approach for spatial proteomics.

PLoS Comput Biol 2018 11 27;14(11):e1006516. Epub 2018 Nov 27.

Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.plos.org/10.1371/journal.pcbi.1006516
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http://dx.doi.org/10.1371/journal.pcbi.1006516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258510PMC
November 2018

Early Responses to Severe Drought Stress in the Cell Suspension Culture Proteome.

Proteomes 2018 Oct 2;6(4). Epub 2018 Oct 2.

Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.3390/proteomes6040038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313886PMC
October 2018

Mass spectrometry approaches to study plant endomembrane trafficking.

Semin Cell Dev Biol 2018 08 13;80:123-132. Epub 2017 Nov 13.

Cambridge Centre for Proteomics, Department of Biochemistry, And Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10849521173046
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http://dx.doi.org/10.1016/j.semcdb.2017.10.014DOI Listing
August 2018

Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency.

EMBO Rep 2018 08 12;19(8). Epub 2018 Jun 12.

Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK

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http://dx.doi.org/10.15252/embr.201745642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6073214PMC
August 2018

Proteomic Comparison of Various Hepatic Cell Cultures for Preclinical Safety Pharmacology.

Toxicol Sci 2018 07;164(1):229-239

Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria 0007, South Africa.

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http://dx.doi.org/10.1093/toxsci/kfy084DOI Listing
July 2018

Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.

Bioinformatics 2018 06;34(11):1884-1892

Department of Computer Science, Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972588PMC
June 2018

Stat3-mediated alterations in lysosomal membrane protein composition.

J Biol Chem 2018 03 17;293(12):4244-4261. Epub 2018 Jan 17.

From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,

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http://dx.doi.org/10.1074/jbc.RA118.001777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5868265PMC
March 2018

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, .

Open Biol 2017 09;7(9)

Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK

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http://dx.doi.org/10.1098/rsob.170135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627053PMC
September 2017

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

Nat Protoc 2017 Jun 4;12(6):1110-1135. Epub 2017 May 4.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nprot.2017.026DOI Listing
June 2017

Time, space, and disorder in the expanding proteome universe.

Proteomics 2017 04 20;17(7). Epub 2017 Mar 20.

Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201600399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573936PMC
April 2017

SWATH-MS data of proteome dynamics during embryogenesis.

Data Brief 2016 Dec 24;9:771-775. Epub 2016 Oct 24.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K.

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http://dx.doi.org/10.1016/j.dib.2016.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097952PMC
December 2016

SWATH-MS dataset of heat-shock treated embryos.

Data Brief 2016 Dec 16;9:991-995. Epub 2016 Nov 16.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K.

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http://dx.doi.org/10.1016/j.dib.2016.11.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123040PMC
December 2016

A Bioconductor workflow for processing and analysing spatial proteomics data.

F1000Res 2016 28;5:2926. Epub 2016 Dec 28.

Computational Proteomics Unit, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.12688/f1000research.10411.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053703PMC
December 2016

Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1.

Biochem J 2016 10 3;473(19):3081-98. Epub 2016 Aug 3.

Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.

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http://www.biochemj.org/content/ppbiochemj/473/19/3081.full.
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http://dx.doi.org/10.1042/BCJ20160593DOI Listing
October 2016

The RNA-binding protein repertoire of Arabidopsis thaliana.

Sci Rep 2016 07 11;6:29766. Epub 2016 Jul 11.

Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1038/srep29766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942612PMC
July 2016

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.

PLoS Comput Biol 2016 05 13;12(5):e1004920. Epub 2016 May 13.

Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866734PMC
May 2016

A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana.

Mol Plant 2016 Apr 30;9(4):621-3. Epub 2015 Nov 30.

Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2015.11.007DOI Listing
April 2016

Analysis of temperature-mediated changes in the wine yeast Saccharomyces bayanus var uvarum. An oenological study of how the protein content influences wine quality.

Proteomics 2016 Feb 25;16(4):576-92. Epub 2016 Jan 25.

Andalusian Center for Grape and Grapevine Research, CeIA3, Marine and Environmental Sciences Faculty, University of Cadiz, Cádiz, Spain.

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http://dx.doi.org/10.1002/pmic.201500137DOI Listing
February 2016

A draft map of the mouse pluripotent stem cell spatial proteome.

Nat Commun 2016 Jan 12;7:8992. Epub 2016 Jan 12.

Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.

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http://dx.doi.org/10.1038/ncomms9992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729960PMC
January 2016

Protein Neighbors and Proximity Proteomics.

Mol Cell Proteomics 2015 Nov 8;14(11):2848-56. Epub 2015 Sep 8.

From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,

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http://dx.doi.org/10.1074/mcp.R115.052902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4638030PMC
November 2015

Drosophila Ionotropic Receptor 25a mediates circadian clock resetting by temperature.

Nature 2015 Nov 18;527(7579):516-20. Epub 2015 Nov 18.

Department of Cell and Developmental Biology, University College London, 21 University Street, London WC1E 6DE, UK.

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https://www.repository.cam.ac.uk/bitstream/handle/1810/25339
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http://www.nature.com/doifinder/10.1038/nature16148
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http://dx.doi.org/10.1038/nature16148DOI Listing
November 2015

α-Klotho Expression in Human Tissues.

J Clin Endocrinol Metab 2015 Oct 17;100(10):E1308-18. Epub 2015 Aug 17.

Renal Division (K.L., T.L., L.-L.H.), Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115; Cambridge Centre for Proteomics (A.G., K.S.L., T.F.H.), and School of Clinical Medicine (I.B.W., T.F.H.), University of Cambridge, Cambridge CB2 0QQ, United Kingdom; Department of Pathology (D.S., S.J., S.T.), University Hospitals Coventry and Warwickshire, NHS Trust, Coventry CV2 2DX, United Kingdom; and Division of Translational Research (G.M., D.Z.), Warwick Medical School, University of Warwick, Coventry CV2 2DX, United Kingdom.

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http://dx.doi.org/10.1210/jc.2015-1800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596032PMC
October 2015

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells.

Stem Cells 2015 Sep 23;33(9):2712-25. Epub 2015 Jun 23.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/stem.2067
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http://dx.doi.org/10.1002/stem.2067DOI Listing
September 2015

Focus on Quantitative Proteomics.

Proteomics 2015 Sep;15(18):3101-3

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http://dx.doi.org/10.1002/pmic.201570163DOI Listing
September 2015

Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.

Proteomics 2015 Jul 17;15(14):2447-57. Epub 2015 Apr 17.

Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, UK.

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http://dx.doi.org/10.1002/pmic.201400530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692092PMC
July 2015

The chicken B-cell line DT40 proteome, beadome and interactomes.

Data Brief 2015 Jun 13;3:29-33. Epub 2015 Jan 13.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.

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http://dx.doi.org/10.1016/j.dib.2014.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509924PMC
June 2015

Analysis of Quality-Related Parameters in Mature Kernels of Polygalacturonase Inhibiting Protein (PGIP) Transgenic Bread Wheat Infected with Fusarium graminearum.

J Agric Food Chem 2015 Apr 9;63(15):3962-9. Epub 2015 Apr 9.

†Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy.

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http://dx.doi.org/10.1021/jf506003tDOI Listing
April 2015

Mep72, a metzincin protease that is preferentially secreted by biofilms of Pseudomonas aeruginosa.

J Bacteriol 2015 Feb 8;197(4):762-73. Epub 2014 Dec 8.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

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http://dx.doi.org/10.1128/JB.02404-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334185PMC
February 2015

SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture.

J Proteomics 2015 Feb 20;115:143-56. Epub 2014 Dec 20.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2014.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329988PMC
February 2015

Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification.

Methods Mol Biol 2014 ;1156:157-74

Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK,

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http://dx.doi.org/10.1007/978-1-4939-0685-7_10DOI Listing
December 2014

Toward a comprehensive map of the effectors of rab GTPases.

Dev Cell 2014 Nov 10;31(3):358-373. Epub 2014 Nov 10.

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807140065
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http://dx.doi.org/10.1016/j.devcel.2014.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232348PMC
November 2014

Label-free protein quantification for plant Golgi protein localization and abundance.

Plant Physiol 2014 Oct 13;166(2):1033-43. Epub 2014 Aug 13.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom

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http://dx.doi.org/10.1104/pp.114.245589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213074PMC
October 2014

A foundation for reliable spatial proteomics data analysis.

Mol Cell Proteomics 2014 Aug 20;13(8):1937-52. Epub 2014 May 20.

From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom;

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http://dx.doi.org/10.1074/mcp.M113.036350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125728PMC
August 2014

Deciphering thylakoid sub-compartments using a mass spectrometry-based approach.

Mol Cell Proteomics 2014 Aug 28;13(8):2147-67. Epub 2014 May 28.

From the ‡Univ. Grenoble Alpes, F-38000 Grenoble, France; **CEA, iRTSV, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France; ‡‡ INSERM, U1038, F-38054 Grenoble, France;

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http://dx.doi.org/10.1074/mcp.M114.040923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125743PMC
August 2014

Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS).

J Proteome Res 2014 Jul 16;13(7):3360-9. Epub 2014 Jun 16.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge , Cambridge, U.K.

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http://dx.doi.org/10.1021/pr500220gDOI Listing
July 2014

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.

Bioinformatics 2014 May 11;30(9):1322-4. Epub 2014 Jan 11.

Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France.

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http://dx.doi.org/10.1093/bioinformatics/btu013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998135PMC
May 2014

New insights into the DT40 B cell receptor cluster using a proteomic proximity labeling assay.

J Biol Chem 2014 May 4;289(21):14434-47. Epub 2014 Apr 4.

From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, the Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge CB2 1QW, United Kingdom,

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http://dx.doi.org/10.1074/jbc.M113.529578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031500PMC
May 2014

Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal.

Nat Biotechnol 2014 May 13;32(5):465-72. Epub 2014 Apr 13.

1] Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK. [2] Department of Chemistry, University of Cambridge, Cambridge, England, UK.

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http://dx.doi.org/10.1038/nbt.2860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107302PMC
May 2014

The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics.

F1000Res 2013 13;2:272. Epub 2013 Dec 13.

Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK ; Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, NW7 1AA, UK.

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http://dx.doi.org/10.12688/f1000research.2-272.v2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983906PMC
April 2014

A protocol for the subcellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation.

Yeast 2014 Apr 20;31(4):127-35. Epub 2014 Feb 20.

Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, UK.

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http://dx.doi.org/10.1002/yea.3002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282465PMC
April 2014

Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry.

Methods Mol Biol 2013 ;1061:291-307

Department of Chemical Engineering and Biotechnology, Cambridge Centre for Neuropsychiatric Research, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-62703-589-7_18DOI Listing
March 2014

Dynamic regulation of the COP9 signalosome in response to DNA damage.

Mol Cell Biol 2014 Mar 13;34(6):1066-76. Epub 2014 Jan 13.

Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1128/MCB.01598-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958043PMC
March 2014

Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue.

J Proteome Res 2014 Feb 17;13(2):763-76. Epub 2014 Jan 17.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1021/pr4008464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929368PMC
February 2014

Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE).

Curr Protoc Protein Sci 2014 Feb 3;75:Unit 22.2.. Epub 2014 Feb 3.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/0471140864.ps2202s75DOI Listing
February 2014

Improving qualitative and quantitative performance for MS(E)-based label-free proteomics.

J Proteome Res 2013 Jun 17;12(6):2340-53. Epub 2013 Apr 17.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1021/pr300776tDOI Listing
June 2013

Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies.

J Proteome Res 2013 Jun 2;12(6):2323-39. Epub 2013 May 2.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, United Kingdom.

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http://dx.doi.org/10.1021/pr300775kDOI Listing
June 2013

Interlaboratory studies and initiatives developing standards for proteomics.

Proteomics 2013 Mar 19;13(6):904-9. Epub 2013 Feb 19.

Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.

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http://dx.doi.org/10.1002/pmic.201200532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863631PMC
March 2013

A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis.

New Phytol 2013 Feb 17;197(3):805-14. Epub 2012 Dec 17.

School of Biological Science, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK.

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http://dx.doi.org/10.1111/nph.12077DOI Listing
February 2013

Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.

Mol Cell Proteomics 2013 Jan 15;12(1):1-13. Epub 2012 Oct 15.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, UK.

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http://dx.doi.org/10.1074/mcp.R112.019554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536891PMC
January 2013

Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins.

Cell Commun Signal 2013 Jan 5;11(1). Epub 2013 Jan 5.

Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/1478-811X-11-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544604PMC
January 2013

Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling.

J Proteomics 2012 Dec 16;77:441-54. Epub 2012 Oct 16.

Centre for Proteomics, Cambridge System Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, UK.

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http://dx.doi.org/10.1016/j.jprot.2012.09.020DOI Listing
December 2012

Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics.

Plant Physiol 2012 Oct 24;160(2):1037-51. Epub 2012 Aug 24.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.

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http://dx.doi.org/10.1104/pp.112.204263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461528PMC
October 2012

Isobaric tagging approaches in quantitative proteomics: the ups and downs.

Anal Bioanal Chem 2012 Sep 12;404(4):1029-37. Epub 2012 May 12.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1007/s00216-012-6012-9DOI Listing
September 2012

MRMaid 2.0: mining PRIDE for evidence-based SRM transitions.

OMICS 2012 Sep 17;16(9):483-8. Epub 2012 Jul 17.

Cranfield Bioinformatics Group, Cranfield Health, Cranfield University, Bedfordshire, UK.

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http://dx.doi.org/10.1089/omi.2011.0143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437039PMC
September 2012

Evaluation and properties of the budding yeast phosphoproteome.

Mol Cell Proteomics 2012 Jun 27;11(6):M111.009555. Epub 2012 Jan 27.

Cambridge Systems Biology Centre and Dept Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M111.009555
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http://dx.doi.org/10.1074/mcp.M111.009555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433898PMC
June 2012

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.

Bioinformatics 2012 Jan 22;28(2):288-9. Epub 2011 Nov 22.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr645DOI Listing
January 2012

LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies.

Anal Chem 2011 Dec 16;83(24):9267-72. Epub 2011 Nov 16.

Laboratorio Biotecnologie Unità Tecnica BIORAD, ENEA CR Casaccia, Roma, Italy.

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http://dx.doi.org/10.1021/ac201733mDOI Listing
December 2011

Uromodulin exclusion list improves urinary exosomal protein identification.

J Biomol Tech 2011 Dec;22(4):136-45

Department of Medical Genetics and Division of Renal Medicine, University of Cambridge, Cambridge, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221452PMC
December 2011

Taming the isobaric tagging elephant in the room in quantitative proteomics.

Nat Methods 2011 Oct 28;8(11):911-3. Epub 2011 Oct 28.

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http://dx.doi.org/10.1038/nmeth.1736DOI Listing
October 2011

ABRF-PRG07: advanced quantitative proteomics study.

J Biomol Tech 2011 Apr;22(1):21-6

University of California-HHMI Mass Spectrometry Lab, Berkeley, California 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059538PMC
April 2011

Challenges for proteomics core facilities.

Proteomics 2011 Mar 16;11(6):1017-25. Epub 2011 Feb 16.

Cambridge Centre for Proteomics, Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000693DOI Listing
March 2011

Proteomic approaches to the characterization of protein thiol modification.

Curr Opin Chem Biol 2011 Feb 2;15(1):120-8. Epub 2010 Dec 2.

MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom.

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https://linkinghub.elsevier.com/retrieve/pii/S13675931100016
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http://dx.doi.org/10.1016/j.cbpa.2010.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087609PMC
February 2011

Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions.

Proteomics 2010 Dec;10(23):4213-9

Anne McLaren Laboratory for Regenerative Medicine and Department of Surgery, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000359DOI Listing
December 2010

Proteomics of total membranes and subcellular membranes.

Expert Rev Proteomics 2010 Dec;7(6):867-78

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://www.tandfonline.com/doi/full/10.1586/epr.10.85
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http://dx.doi.org/10.1586/epr.10.85DOI Listing
December 2010

Organelle proteomics experimental designs and analysis.

Proteomics 2010 Nov 2;10(22):3957-69. Epub 2010 Nov 2.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000244DOI Listing
November 2010