Dr Trong Khoa Pham
MSc, PhD, FHEA
School of Biosciences
Biological Mass Spectrometry Facility Manager
Expertise: Proteomics
khoa.pham@sheffield.ac.uk
+44 114 222 4676
+44 114 222 4676
B11f, Dainton Building
Full contact details
Dr Trong Khoa Pham
School of Biosciences
B11f
Dainton Building
13 Brook Hill
Sheffield
S3 7HF
School of Biosciences
B11f
Dainton Building
13 Brook Hill
Sheffield
S3 7HF
- Research interests
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With over fifteen years of experience in biological mass spectrometry analyses, I am passionate about using these tools to enhance our understanding and improving of biological processes, and discover new biomarkers.
I specialise in proteomics analysis, including method development, identification and characterization of both small and large molecules (metabolites, peptides, and proteins), as well as post-translational modification (PTM) analysis (e.g. phosphorylation, methylation, acetylation, and glycosylation), relative and absolute quantitation (LFQ and multiplexing), and protein interaction in biological samples (specimens).
Throughout my career, I have collaborated with researchers and academics on numerous projects, contributing to many successful initiatives. I am always looking to expand my collaborative networks, both nationally and internationally, and welcome opportunities to work with partners to advance our understanding of the complex biological systems that shape our world.
- Publications
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Journal articles
- Proteomic approaches to study cysteine oxidation: applications in neurodegenerative diseases. Frontiers in Molecular Neuroscience, 14.
- Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources. Biotechnology for Biofuels, 14(1).
- Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress. Applied and Environmental Microbiology, 87(11).
- Identification of Copper-Binding Peptides and Investigation of Functional Properties of Acetes japonicus Proteolysate. Waste and Biomass Valorization, 12(3), 1565-1579.
- Phosphopeptide enrichment for phosphoproteomic analysis - a tutorial and review of novel materials. Analytica Chimica Acta, 1129, 158-180.
- Copper-chelating peptide from salmon by-product proteolysate. International Journal of Food Engineering, 16(4).
- Evaluation of iron-binding capacity, amino acid composition, functional properties of Acetes japonicus proteolysate and identification of iron-binding peptides. Process Biochemistry, 91, 374-386.
- Alcoholic fermentation of thermochemical and biological hydrolysates derived from Miscanthus biomass by Clostridium acetobutylicum ATCC 824. Biomass and Bioenergy, 130, 105382-105382.
- CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels. Algal Research, 41, 101510-101510.
- Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius. Journal of Biological Chemistry, 294(18), 7460-7471.
- Identification of a new calcium‐binding peptide from enzymatic proteolysate of
Acetes japonicus. Journal of Food Processing and Preservation, 42(12), e13837-e13837.
- Characterisation and pure culture of putative health-associated oral bacterium BU063 (Tannerella sp. HOT-286) reveals presence of a potentially novel glycosylated S-layer. FEMS Microbiology Letters, 365(17).
- Natural mutagenesis-enabled global proteomic study of metabolic and carbon source implications in mutant thermoacidophillic Archaeon Sulfolobus solfataricus PBL2025. Journal of Proteome Research.
- Oxidative Stickland reactions in an obligate aerobic organism – amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus. The FEBS Journal.
- A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Molecular Microbiology.
- An iTRAQ characterisation of the role of TolC during electron transfer from Shewanella oneidensis MR-1.. Proteomics.
- Protein phosphorylation and its role in archaeal signal transduction. FEMS Microbiology Reviews, [Epub ahead of print].
- Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824. Biotechnology for Biofuels, 9(1).
- Quantitative analysis of UV-A shock and short term stress using iTRAQ, pseudo selective reaction monitoring (pSRM) and GC-MS based metabolite analysis of the cyanobacterium Nostoc punctiforme ATCC 29133. Journal of Proteomics, 109, 332-355.
- A cool tool for hot and sour Archaea: proteomics of Sulfolobus solfataricus.. Proteomics, 13(18-19), 2831-2850.
- Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in Sulfolobus acidocaldarius.. Mol Cell Proteomics, 12(12), 3908-3923.
- Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode.. J Proteomics, 78, 197-210.
- Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus. Journal of Proteome Research, 11(10), 4823-4833.
- Bioinformatic study of the relationship between protein regulation and sequence properties.. Genomics, 100(4), 240-244.
- An insight into iTRAQ: where do we stand now?. Anal Bioanal Chem, 404(4), 1011-1027.
- Macromolecular Fingerprinting of Sulfolobus Species in Biofilm: A Transcriptomic and Proteomic Approach Combined with Spectroscopic Analysis. J PROTEOME RES, 10(9), 4105-4119.
- Proteomic evaluation and validation of cathepsin D regulated proteins in macrophages exposed to Streptococcus pneumoniae.. Mol Cell Proteomics, 10(6), M111.008193.
- Methods in quantitative proteomics: Setting iTRAQ on the right track. Current Proteomics, 8(1), 17-30.
- A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen Tannerella forsythia.. Proteomics, 10(17), 3130-3141.
- Quantitative proteomic analysis of Sulfolobus solfataricus membrane proteins.. J Proteome Res, 9(2), 1165-1172.
- "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus. EXTREMOPHILES, 14(1), 119-142.
- SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. BIOCHEMICAL SOCIETY TRANSACTIONS, 37, 58-64.
- The proteomic response of Saccharomyces cerevisiae in very high glucose conditions with amino acid supplementation.. J Proteome Res, 7(11), 4766-4774.
- Proteomic analysis of calcium alginate-immobilized Saccharomyces cerevisiae under high-gravity fermentation conditions.. J Proteome Res, 7(2), 515-525.
- Proteomic analysis of Saccharomyces cerevisiae.. Expert Rev Proteomics, 4(6), 793-813.
- Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: Implication of multiple injections.. J Proteome Res, 5(5), 1232-1240.
- Proteomic analysis of Saccharomyces cerevisiae under high gravity fermentation conditions. J Proteome Res, 5(12), 3411-3419.
- Earthworm (Perionyx excavatus) Protein Hydrolysate: Hypoglycemic Activity and Its Stability for the Hydrolysate and Its Peptide Fractions. Processes, 11(8), 2490-2490.
- Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Frontiers in Microbiology, 9.
- Protein Profiling of the Secretome of FcεRI Activated RBL-2H3.1 Cells. Iran J Immunol, 9(1), 1-31.
Conference proceedings papers
- Quantitative proteomic analysis of membrane proteins based on gel and shotgun techniques. AIChE Annual Meeting, Conference Proceedings
Posters
- Improved understanding of protein phosphorylation in Sulfolobus species. 60th ASMS Conference on Mass Spectrometry and Allied Topics Vancouver, BC, Canada.
- Quantitative proteomic analysis of the archaeon Sulfolobus solfataricus P2: Hot life at lower temperatures. 4th EuPA meeting, Estoril, Portugal.
- Regulation of central carbon metabolism in the archaeon, Sulfolobus solfataricus P2 under temperature variations: A quantitative proteomic aspect. BESG Young Researchers Meeting, Institute of Chemical Engineers (IChemE), University of Cambridge, U.
- Proteomic analysis of Sulfolobus solfataricus P2. 2nd SYSMO Evaluation Conference, Vienna, Austria.
- Sulfolobus solfataricus: The life under high temperature. BESG Young Researchers Meeting, IChemE, The University of Sheffield, UK.
- Proteomic approaches to study cysteine oxidation: applications in neurodegenerative diseases. Frontiers in Molecular Neuroscience, 14.