Multidimensional Proteomic Analysis of Metabolic Stress & Cellular Phenotypes (Strategic Grant)

Cantrell, Doreen (Investigator)
Lamond, Angus (Investigator)

42 Article
1 Letter
1 Review article
1 Preprint

45 results

2024
Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples
Baker, C. P., Bruderer, R., Abbott, J., Arthur, J. S. C. (Lead / Corresponding author) & Brenes Murillo, A. J. (Lead / Corresponding author), 7 Jun 2024, In: Journal of Proteome Research. 23, 6, p. 1926-1936 11 p.
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Proteomic and functional comparison between human induced and embryonic stem cells
Brenes Murillo, A., Griesser, E., Sinclair, L., Davidson, L., Prescott, A., Singh, F., Hogg, E., Espejo-Serrano, C., Jiang, H., Yoshikawa, H., Platani, M., Swedlow, J., Findlay, G., Cantrell, D. & Lamond, A. (Lead / Corresponding author), 14 Nov 2024, In: eLife. 13, p. 1-32 32 p.
Research output: Contribution to journal › Article › peer-review

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2023
Proteomic and functional comparison between human induced and embryonic stem cells
Brenes Murillo, A., Griesser, E., Sinclair, L., Davidson, L., Prescott, A., Singh, F., Hogg, E., Espejo-Serrano, C., Jiang, H., Yoshikawa, H., Platani, M., Swedlow, J., Findlay, G., Cantrell, D. & Lamond, A. (Lead / Corresponding author), 19 Aug 2023, BioRxiv, 34 p.
Research output: Working paper/Preprint › Preprint

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2022
Nrf2 activation reprograms macrophage intermediary metabolism and suppresses the type I interferon response
Ryan, D. G., Knatko, E. V., Casey, A. M., Hukelmann, J., Dayalan Naidu, S., Brenes, A. J., Ekkunagul, T., Baker, C., Higgins, M., Tronci, L., Nikitopolou, E., Honda, T., Hartley, R. C., O'Neill, L. A. J., Frezza, C., Lamond, A. I., Abramov, A. Y., Arthur, J. S. C., Cantrell, D. A. & Murphy, M. P. & 1 others, Dinkova-Kostova, A. T. (Lead / Corresponding author), 18 Feb 2022, In: iScience. 25, 2, 21 p., 103827.
Research output: Contribution to journal › Article › peer-review

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2021
Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Brenes, A. J. (Lead / Corresponding author), Yoshikawa, H., Bensaddek, D., Mirauta, B., Seaton, D. D., Hukelmann, J., Jiang, H., Stegle, O. & Lamond, A., 27 Apr 2021, In: Cell Reports. 35, 4, 20 p., 109032.
Research output: Contribution to journal › Article › peer-review

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Extracellular signal-regulated kinase (ERK) pathway control of CD8⁺ T cell differentiation
Damasio, M. P., Marchingo, J. M., Spinelli, L., Hukelmann, J. L., Cantrell, D. A. (Lead / Corresponding author) & Howden, A. J. M. (Lead / Corresponding author), 13 Jan 2021, In: Biochemical Journal. 478, 1, p. 79-98 20 p.
Research output: Contribution to journal › Article › peer-review

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Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes
Brenes, A., Vandereyken, M., James, O. J., Watt, H., Hukelmann, J., Spinelli, L., Dikovskaya, D., Lamond, A. I. & Swamy, M. (Lead / Corresponding author), 24 Sept 2021, In: eLife. 10, 28 p., e70055.
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2020
Population-scale proteome variation in human induced pluripotent stem cells
Mirauta, B. A., Seaton, D. D., Bensaddek, D., Brenes Murillo, A., Bonder, M. J., Kilpinen, H., HipSci Consortium, Stegle, O. (Lead / Corresponding author) & Lamond, A. I. (Lead / Corresponding author), 25 Aug 2020, In: eLife. 9, 22 p., e57390.
Research output: Contribution to journal › Article › peer-review

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2019
Antigen receptor control of methionine metabolism in T cells
Sinclair, L. V. (Lead / Corresponding author), Howden, A., Brenes Murillo, A., Spinelli, L., Hukelmann, J., Macintyre, A. N., Liu, X., Thomson, S., Taylor, P., Rathmell, J. C., Locasale, J. W., Lamond, A. & Cantrell, D. A. (Lead / Corresponding author), 27 Mar 2019, In: eLife. 8, p. 1-29 29 p., e44210.
Research output: Contribution to journal › Article › peer-review

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Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster
Matera, A. G. (Lead / Corresponding author), Raimer, A. C., Schmidt, C. A., Kelly, J. A., Droby, G. N., Baillat, D., Ten Have, S., Lamond, A. I., Wagner, E. J. & Gray, K. M., 1 Feb 2019, In: G3: Genes | Genomes | Genetics. 9, 2, p. 491-503 13 p.
Research output: Contribution to journal › Article › peer-review

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EMSY expression affects multiple components of the skin barrier with relevance to atopic dermatitis
Elias, M. S. (Lead / Corresponding author), Wright, S. C., Remenyi, J., Abbott, J. C., Bray, S. E., Cole, C., Edwards, S., Gierlinski, M., Glok, M., McGrath, J. A., Nicholson, W. V., Paternoster, L., Prescott, A. R., Have, S. T., Whitfield, P. D., Lamond, A. I. & Brown, S. J. (Lead / Corresponding author), Aug 2019, In: Journal of Allergy and Clinical Immunology. 144, 2, p. 470-481 12 p.
Research output: Contribution to journal › Article › peer-review

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Functional and proteomic analysis of a full thickness filaggrin-deficient skin organoid model
Elias, M. S., Wright, S. C., Nicholson, W. V., Morrison, K. D., Prescott, A. R., Ten Have, S., Whitfield, P. D., Lamond, A. I. & Brown, S. J., 9 Sept 2019, (E-pub ahead of print) In: Wellcome Open Research. 4, p. 134 28 p.
Research output: Contribution to journal › Article › peer-review

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Multi-batch TMT reveals false positives, batch effects and missing values
Brenes Murillo, A., Hukelmann, J., Bensaddek, D. & Lamond, A. (Lead / Corresponding author), 1 Oct 2019, In: Molecular and Cellular Proteomics. 18, 10, p. 1967-1980 14 p.
Research output: Contribution to journal › Article › peer-review

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Proteome turnover in the bloodstream and procyclic forms of Trypanosoma brucei measured by quantitative proteomics
Tinti, M. (Lead / Corresponding author), Güther, M. L. S., Crozier, T. W. M., Lamond, A. I. & Ferguson, M. A. J., 9 Oct 2019, In: Wellcome Open Research. 4, p. 1-27 27 p., 152.
Research output: Contribution to journal › Article › peer-review

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Proteomic analysis of a filaggrin-deficient skin organoid model shows evidence of increased transcriptional-translational activity, keratinocyte-immune crosstalk and disordered axon guidance
Elias, M. S. (Lead / Corresponding author), Wright, S. C., Nicholson, W. V., Morrison, K. D., Prescott, A. R., Ten Have, S., Whitfield, P. D., Lamond, A. I. & Brown, S. J., 30 Sept 2019, (E-pub ahead of print) In: Wellcome Open Research. 4, p. 1-21 21 p., 134.
Research output: Contribution to journal › Article › peer-review

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Quantitative analysis of T cell proteomes and environmental sensors during T cell differentiation
Howden, A. J. M., Hukelmann, J. L., Brenes, A., Spinelli, L., Sinclair, L. V., Lamond, A. I. (Lead / Corresponding author) & Cantrell, D. A. (Lead / Corresponding author), Nov 2019, In: Nature Immunology. 20, 11, p. 1542-1554 13 p.
Research output: Contribution to journal › Article › peer-review

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Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes
Bensaddek, D., Nicolas, A. & Lamond, A. I. (Lead / Corresponding author), Feb 2019, In: Current Opinion in Chemical Biology. 48, p. 114-122 9 p.
Research output: Contribution to journal › Review article › peer-review

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The Encyclopedia of Proteome Dynamics: The KinoViewer
Brenes Murillo, A. & Lamond, A., 15 Apr 2019, In: Bioinformatics. 35, 8, p. 1441-1442 2 p., bty823.
Research output: Contribution to journal › Article › peer-review

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2018
8-Aryl-6-chloro-3-nitro-2-(phenylsulfonylmethyl)imidazo[1,2-a]pyridines as potent antitrypanosomatid molecules bioactivated by type 1 nitroreductases
Fersing, C., Boudot, C., Pedron, J., Hutter, S., Primas, N., Castera-Ducros, C., Bourgeade-Delmas, S., Sournia-Saquet, A., Moreau, A., Cohen, A., Stigliani, J.-L., Pratviel, G., Crozet, M. D., Wyllie, S., Fairlamb, A., Valentin, A., Rathelot, P., Azas, N., Courtioux, B. & Verhaeghe, P. & 1 others, Vanelle, P. (Lead / Corresponding author), 5 Sept 2018, In: European Journal of Medicinal Chemistry. 157, p. 115-126 12 p.
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Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice
Loftus, R. M., Assmann, N., Kedia-Mehta, N., O'Brien, K. L., Garcia, A., Gillespie, C., Hukelmann, J. L., Oefner, P. J., Lamond, A. I., Gardiner, C. M., Dettmer, K., Cantrell, D. A., Sinclair, L. V. & Finlay, D. K. (Lead / Corresponding author), 14 Jun 2018, In: Nature Communications. 9, 1, p. 1-15 15 p., 2341.
Research output: Contribution to journal › Article › peer-review

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An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis
Liakath-Ali, K., Mills, E. W., Sequeira, I., Lichtenberger, B. M., Pisco, A. O., Sipilä, K. H., Mishra, A., Yoshikawa, H., Wu, C.C.-C., Ly, T., Lamond, A. I., Adham, I. M., Green, R. & Watt, F. M. (Lead / Corresponding author), 11 Apr 2018, In: Nature. 556, p. 376-380 5 p.
Research output: Contribution to journal › Letter › peer-review

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Efficient Analysis of Mammalian Polysomes in cells and tissues using Ribo Mega-SEC
Yoshikawa, H., Larance, M., Harney, D. J., Sundaramoorthy, R., Ly, T., Owen-Hughes, T. & Lamond, A. I. (Lead / Corresponding author), 10 Aug 2018, In: eLife. 7, 7, p. 1-26 26 p., e36530.
Research output: Contribution to journal › Article › peer-review

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PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ
Jonik-Nowak, B., Menneteau, T., Fesquet, D., Baldin, V., Bonne-Andrea, C., Méchali, F., Fabre, B., Boisguerin, P., de Rossi, S., Henriquet, C., Pugnière, M., Ducoux-Petit, M., Burlet-Schiltz, O., Lamond, A., Fort, P., Boulon, S. (Lead / Corresponding author), Bousquet, M.-P. (Lead / Corresponding author) & Coux, O., 10 Jul 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. E6477-E6486 10 p., 201722299.
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Proteome-wide analysis of protein abundance and turnover remodelling during oncogenic transformation of human breast epithelial cells
Ly, T., Endo, A., Brenes, A., Gierlinski, M., Afzal, V., Pawellek, A. & Lamond, A. I. (Lead / Corresponding author), 2 May 2018, In: Wellcome Open Research. 3, p. 1-48 48 p., 51.
Research output: Contribution to journal › Article › peer-review

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Proteomic analysis of the cell cycle of procylic form Trypanosoma brucei
Crozier, T. W. M., Tinti, M., Wheeler, R. J., Ly, T., Ferguson, M. A. J. & Lamond, A. I. (Lead / Corresponding author), 1 Jun 2018, In: Molecular & Cellular Proteomics. 17, 6, p. 1184-1195 12 p.
Research output: Contribution to journal › Article › peer-review

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Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF^Slmb degron
Gray, K. M., Kaifer, K. A., Baillat, D., Wen, Y., Bonacci, T. R., Ebert, A. D., Raimer, A. C., Spring, A. M., Have, S. T., Glascock, J. J., Gupta, K., Van Duyne, G. D., Emanuele, M. J., Lamond, A. I., Wagner, E. J., Lorson, C. L. & Matera, A. G. (Lead / Corresponding author), 15 Jan 2018, In: Molecular Biology of the Cell. 29, 2, p. 96-110 15 p.
Research output: Contribution to journal › Article › peer-review

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The Encyclopedia of Proteome Dynamics – A big data ecosystem for (prote)omics
Brenes Murillo, A., Afzal, V., Kent, R. & Lamond, A. (Lead / Corresponding author), 4 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D1202-D1209 8 p.
Research output: Contribution to journal › Article › peer-review

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2017
A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis
Mishra, A., Oulès, B., Pisco, A. O., Ly, T., Liakath-Ali, K., Walko, G., Viswanathan, P., Tihy, M., Nijjhar, J., Dunn, S.-J., Lamond, A. I. & Watt, F. M. (Lead / Corresponding author), 18 Oct 2017, In: eLife. 6, p. 1-20 20 p., e27356.
Research output: Contribution to journal › Article › peer-review

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Characterisation of the biflavonoid hinokiflavone as a premRNA splicing modulator that inhibits SENP
Pawellek, A., Ryder, U., Tammsalu, T., King, L. J., Kreinin, H., Ly, T., Hay, R. T., Hartley, R. & Lamond, A. (Lead / Corresponding author), 8 Sept 2017, In: eLife. 6, e27402.
Research output: Contribution to journal › Article › peer-review

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Common genetic variation drives molecular heterogeneity in human iPSCs
Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., Danecek, P., Faulconbridge, A., Harrison, P. W., Kathuria, A., McCarthy, D. J., McCarthy, S. A., Meleckyte, R., Memari, Y., Moens, N. & Soares, F. & 23 others, Mann, A., Streeter, I., Agu, C. A., Alderton, A., Nelson, R., Harper, S., Patel, M., White, A., Patel, S. R., Clarke, L., Halai, R., Kirton, C. M., Kolb-Kokocinski, A., Beales, P. L., Birney, E., Danovi, D., Lamond, A. I., Ouwehand, W. H., Vallier, L., Watt, F. M. (Lead / Corresponding author), Durbin, R. (Lead / Corresponding author), Stegle, O. (Lead / Corresponding author) & Gaffney, D. J. (Lead / Corresponding author), 15 Jun 2017, In: Nature. 546, 7658, p. 370-375 6 p.
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Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development
Offenburger, S.-L., Bensaddek, D., Brenes Murillo, A., Lamond, A. I. & Gartner, A. (Lead / Corresponding author), 28 Jun 2017, In: Scientific Reports. 7, p. 1-17 17 p., 4314.
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Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation
Hiraga, S.-I. (Lead / Corresponding author), Ly, T., Garzón, J., Hořejší, Z., Ohkubo, Y.-N., Endo, A., Obuse, C., Boulton, S. J., Lamond, A. & Donaldson, A. D. (Lead / Corresponding author), 1 Mar 2017, In: EMBO Reports. 18, 3, p. 403-419 17 p.
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Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans
Harvald, E. B., Sprenger, R. R., Dall, K. B., Ejsing, C. S., Nielsen, R., Mandrup, S., Brenes Murillo, A., Larance, M., Gartner, A., Lamond, A. & Færgeman, N. J. (Lead / Corresponding author), 26 Jul 2017, In: Cell Systems. 5, 1, p. 38-52.e4 13 p.
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New Apex in Proteome Analysis
Ly, T. & Lamond, A. I. (Lead / Corresponding author), 28 Jun 2017, In: Cell Systems. 4, 6, p. 581-582 2 p.
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Prediction of protein complexes in Trypanosoma brucei by protein correlation profiling mass spectrometry and machine learning
Crozier, T. W. M., Tinti, M., Larance, M., Lamond, A. I. (Lead / Corresponding author) & Ferguson, M. A. J. (Lead / Corresponding author), 1 Dec 2017, In: Molecular & Cellular Proteomics. 16, 12, p. 2254-2267 14 p.
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Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS
Ly, T. (Lead / Corresponding author), Whigham, A., Clarke, R., Brenes-Murillo, A. J., Estes, B., Madhessian, D., Lundberg, E., Wadsworth, P. & Lamond, A. I. (Lead / Corresponding author), 20 Oct 2017, In: eLife. 6, p. 1-35 35 p., e27574.
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The chromatin assembly factor complex 1 (CAF1) and 5-Azacytidine (5-AzaC) affect cell motility in Src-transformed human epithelial cells
Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. & Lamond, A. I. (Lead / Corresponding author), 6 Jan 2017, In: Journal of Biological Chemistry. 292, 1, p. 172-184 13 p.
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The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Akay, A., Di Domenico, T., Suen, K. M., Nabih, A., Parada, G. E., Larance, M., Medhi, R., Berkyurek, A. C., Zhang, X., Wedeles, C. J., Rudolph, K. L. M., Engelhardt, J., Hemberg, M., Ma, P., Lamond, A. I., Claycomb, J. M. & Miska, E. A. (Lead / Corresponding author), 7 Aug 2017, In: Developmental Cell. 42, 3, p. 241-255.e6 21 p.
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2016
CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells
Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. & Rocha, S. (Lead / Corresponding author), Jan 2016, In: Journal of Cell Science. 129, 1, p. 191-205 15 p.
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Deep Proteome Analysis Identifies Age-Related Processes in C. elegans
Narayan, V., Ly, T., Pourkarimi, E., Brenes Murillo, A., Gartner, A., Lamond, A. & Kenyon, C. (Lead / Corresponding author), 24 Aug 2016, In: Cell Systems. 3, 2, p. 144-159 15 p.
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Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines
Ono, M., Ono, K., Bensaddek, D., Afzal, V., Biddlestone, J., Ortmann, B., Mudie, S., Boivin, V., S. Scott, M., Rocha, S. & Lamond, A. I. (Lead / Corresponding author), 29 Apr 2016, In: PLoS ONE. 11, 4, 28 p., e0154759.
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Global membrane protein interactome analysis using in vivo crosslinking and MS-based protein correlation profiling
Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. & Lamond, A. (Lead / Corresponding author), 1 Jul 2016, In: Molecular & Cellular Proteomics. 15, 7, p. 2476-2490 15 p.
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Micro-proteomics with iterative data analysis: proteome analysis in C.elegans at the single worm level
Bensaddek, D., Narayan, V., Nicolas, A., Brenes Murillo, A., Gartner, A., Kenyon, C. & Lamond, A. (Lead / Corresponding author), 10 Feb 2016, In: Proteomics. 16, 3, p. 381-392
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The cytotoxic T cell proteome and its shaping by the kinase mTOR
Hukelmann, J. L., Anderson, K. E., Sinclair, L. V., Grzes, K. M., Brenes Murillo, A., Hawkins, P. T., Stephens, L. R., Lamond, A. I. & Cantrell, D. A. (Lead / Corresponding author), Jan 2016, In: Nature Immunology. 17, 1, p. 104-112 9 p.
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2015
Evaluating the use of HILIC in large-scale, multi dimensional proteomics: horses for courses?
Bensaddek, D., Nicolas, A. & Lamond, A. I. (Lead / Corresponding author), 30 Nov 2015, In: International Journal of Mass Spectrometry. 391, p. 105-114 10 p.
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Multidimensional Proteomic Analysis of Metabolic Stress & Cellular Phenotypes (Strategic Grant)

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2015