Kai Cheng – NorthOmics

Bioinformatician

ckkazuma[at]gmail.com

Education

July 2015 – July 2020, PostDoc, in University of Ottawa

July 2009 – July 2015, PhD studies, Dalian Institute of Chemical Physics

Publications in NorthOmics

Duong VA, Enkhbayar A, Bhasin N, Senavirathna L, Preisner EC, Hoffman KL, Shukla R, Jenq RR, Cheng K, Bronner MP, Figeys D, Britton RA, Pan S and Chen R. A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies. (2024) Proteomics. e2400078 Pubmed Proteomics

Cheng K, Ning Z, Li L, Zhang X, Serrana JM, Mayne J and Figeys D. MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database. (2023) J Proteome Res. 22, 387-398 Pubmed J Proteome Res PMC Article

Duan H, Cheng K, Ning Z, Li L, Mayne J, Sun Z and Figeys D. Assessing the Dark Field of Metaproteome. (2022) Anal Chem. 94, 15648-15654 Pubmed Anal Chem PMC Article

Li L, Ning Z, Cheng K, Zhang X, Simopoulos CMA and Figeys D. iMetaLab Suite: A one-stop toolset for metaproteomics. (2022) Imeta. 1, e25 Pubmed Imeta PMC Article

Chang L, Lin F, Cheng K, Li J, Sun X, Figeys D, Jiang J, Ye Y and Liu J. A simultaneous identification and quantification strategy for determination of sulfhydryl-containing metabolites in normal- and high-fat diet hamsters using stable isotope labeling combined with LC-MS. (2021) Anal Chim Acta. 1184, 339016 Pubmed Anal Chim Acta

Li H, Zhang X, Chen R, Cheng K, Ning Z, Li J, Twine S, Stintzi A, Mack D and Figeys D. Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis. (2021) J Proteomics. 249, 104369 Pubmed J Proteomics

Zhang X, Cheng K, Ning Z, Mayne J, Walker K, Chi H, Farnsworth CL, Lee K and Figeys D. Exploring the Microbiome-Wide Lysine Acetylation, Succinylation, and Propionylation in Human Gut Microbiota. (2021) Anal Chem. 93, 6594-6598 Pubmed Anal Chem

Hao Z, Li L, Ning Z, Zhang X, Mayne J, Cheng K, Walker K, Liu H and Figeys D. Metaproteomics Reveals Growth Phase-Dependent Responses of an Gut Microbiota to Metformin. (2020) J Am Soc Mass Spectrom. 31, 1448-1458 Pubmed J Am Soc Mass Spectrom

Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J and Figeys D. MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics. (2020) J Am Soc Mass Spectrom. 31, 1473-1482 Pubmed J Am Soc Mass Spectrom

Wang J, Zhang X, Li L, Ning Z, Mayne J, Schmitt-Ulms C, Walker K, Cheng K and Figeys D. Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics. (2020) Anal Chem. 92, 5379-5386 Pubmed Anal Chem

Li L, Ning Z, Zhang X, Mayne J, Cheng K, Stintzi A and Figeys D. RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs. (2020) Microbiome. 8, 33 Pubmed Microbiome PMC Article

Li H, Li L, Cheng K, Ning Z, Mayne J, Zhang X, Walker K, Chen R, Twine S, Li J and Figeys D. Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation. (2020) Anal Chem. 92, 1618-1627 Pubmed Anal Chem

Li L, Abou-Samra E, Ning Z, Zhang X, Mayne J, Wang J, Cheng K, Walker K, Stintzi A and Figeys D. An in vitro model maintaining taxon-specific functional activities of the gut microbiome. (2019) Nat Commun. 10, 4146 Pubmed Nat Commun PMC Article

Liao B, Ning Z, Cheng K, Zhang X, Li L, Mayne J and Figeys D. iMetaLab 1.0: a web platform for metaproteomics data analysis. (2018) Bioinformatics. 34, 3954-3956 Pubmed Bioinformatics

Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, Mayne J, Cheng K, Liao B, Li L, Singleton R, Mack D, Stintzi A and Figeys D. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. (2018) Nat Commun. 9, 2873 Pubmed Nat Commun PMC Article

Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M and Figeys D. Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions. (2018) Anal Chem. 90, 86-109 Pubmed Anal Chem

Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J, Stintzi A and Figeys D. MetaLab: an automated pipeline for metaproteomic data analysis. (2017) Microbiome. 5, 157 Pubmed Microbiome PMC Article

Chen R, Cheng K, Ning Z and Figeys D. N-Glycopeptide Reduction with Exoglycosidases Enables Accurate Characterization of Site-Specific N-Glycosylation. (2016) Anal Chem. 88, 11837-11843 Pubmed Anal Chem

Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI and Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. (2016) Anal Chem. 88, 95-121 Pubmed Anal Chem

Cheng K, Chen R, Seebun D, Ye M, Figeys D and Zou H. Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. (2014) J Proteomics. 110, 145-54 Pubmed J Proteomics

Zhu J, Wang F, Cheng K, Song C, Qin H, Hu L, Figeys D, Ye M and Zou H. Analysis of human serum phosphopeptidome by a focused database searching strategy. (2013) J Proteomics. 78, 389-97 Pubmed J Proteomics

Song C, Wang F, Ye M, Cheng K, Chen R, Zhu J, Tan Y, Wang H, Figeys D and Zou H. Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach. (2011) Anal Chem. 83, 7755-62 Pubmed Anal Chem

Chiang CK, Xu B, Mehta N, Mayne J, Sun WY, Cheng K, Ning Z, Dong J, Zou H, Cheng HM and Figeys D. Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus. (2017) Front Neurol. 8, 110 Pubmed Front Neurol PMC Article

Sun Z, Ning Z, Cheng K, Duan H, Wu Q, Mayne J and Figeys D. MetaPep: A core peptide database for faster human gut metaproteomics database searches. (2023) Comput Struct Biotechnol J. 21, 4228-4237 Pubmed Comput Struct Biotechnol J PMC Article

Previous Publications

Qin H, Cheng K, Zhu J, Mao J, Wang F, Dong M, Chen R, Guo Z, Liang X, Ye M and Zou H. Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy. (2017) Anal Chem. 89, 1469-1476 Pubmed Anal Chem

Bian Y, Li L, Dong M, Liu X, Kaneko T, Cheng K, Liu H, Voss C, Cao X, Wang Y, Litchfield D, Ye M, Li SS and Zou H. Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. (2016) Nat Chem Biol. 12, 959-966 Pubmed Nat Chem Biol

Wu J, Qin H, Li T, Cheng K, Dong J, Tian M, Chai N, Guo H, Li J, You X, Dong M, Ye M, Nie Y, Zou H and Fan D. Characterization of site-specific glycosylation of secreted proteins associated with multi-drug resistance of gastric cancer. (2016) Oncotarget. 7, 25315-27 Pubmed Oncotarget PMC Article

Wang C, Ye M, Wei X, Bian Y, Cheng K and Zou H. A bead-based cleavage method for large-scale identification of protease substrates. (2016) Sci Rep. 6, 22645 Pubmed Sci Rep PMC Article

Li J, Wang F, Wan H, Liu J, Liu Z, Cheng K and Zou H. Magnetic nanoparticles coated with maltose-functionalized polyethyleneimine for highly efficient enrichment of N-glycopeptides. (2015) J Chromatogr A. 1425, 213-20 Pubmed J Chromatogr A

Yao Y, Huang J, Cheng K, Pan Y, Qin H, Ye M and Zou H. Specific Enrichment of Peptides with N-Terminal Serine/Threonine by a Solid-Phase Capture-Release Approach for Efficient Proteomics Analysis. (2015) Anal Chem. 87, 11353-60 Pubmed Anal Chem

Huang J, Wan H, Yao Y, Li J, Cheng K, Mao J, Chen J, Wang Y, Qin H, Zhang W, Ye M and Zou H. Highly Efficient Release of Glycopeptides from Hydrazide Beads by Hydroxylamine Assisted PNGase F Deglycosylation for N-Glycoproteome Analysis. (2015) Anal Chem. 87, 10199-204 Pubmed Anal Chem

Huang J, Qin H, Sun Z, Huang G, Mao J, Cheng K, Zhang Z, Wan H, Yao Y, Dong J, Zhu J, Wang F, Ye M and Zou H. A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method. (2015) Sci Rep. 5, 10164 Pubmed Sci Rep PMC Article

Li J, Wang F, Liu J, Xiong Z, Huang G, Wan H, Liu Z, Cheng K and Zou H. Functionalizing with glycopeptide dendrimers significantly enhances the hydrophilicity of the magnetic nanoparticles. (2015) Chem Commun (Camb). 51, 4093-6 Pubmed Chem Commun (Camb)

Liu J, Wang F, Mao J, Zhang Z, Liu Z, Huang G, Cheng K and Zou H. High-sensitivity N-glycoproteomic analysis of mouse brain tissue by protein extraction with a mild detergent of N-dodecyl β-D-maltoside. (2015) Anal Chem. 87, 2054-7 Pubmed Anal Chem

Cheng K, Wang F, Bian Y, Ye M and Zou H. [Identifying phosphopeptide by searching a site annotated protein database]. (2015) Se Pu. 33, 10-6 Pubmed Se Pu

Wang K, Zhou YJ, Liu H, Cheng K, Mao J, Wang F, Liu W, Ye M, Zhao ZK and Zou H. Proteomic analysis of protein methylation in the yeast Saccharomyces cerevisiae. (2015) J Proteomics. 114, 226-33 Pubmed J Proteomics

Dong M, Ye M, Cheng K, Dong J, Zhu J, Qin H, Bian Y and Zou H. Identification of phosphopeptides with unknown cleavage specificity by a de novo sequencing assisted database search strategy. (2014) Proteomics. 14, 2410-6 Pubmed Proteomics

Pan Y, Cheng K, Mao J, Liu F, Liu J, Ye M and Zou H. Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion. (2014) Anal Bioanal Chem. 406, 6247-56 Pubmed Anal Bioanal Chem

Huang J, Qin H, Dong J, Song C, Bian Y, Dong M, Cheng K, Wang F, Sun D, Wang L, Ye M and Zou H. In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis. (2014) J Proteome Res. 13, 3896-904 Pubmed J Proteome Res

Xu B, Wang F, Song C, Sun Z, Cheng K, Tan Y, Wang H and Zou H. Large-scale proteome quantification of hepatocellular carcinoma tissues by a three-dimensional liquid chromatography strategy integrated with sample preparation. (2014) J Proteome Res. 13, 3645-54 Pubmed J Proteome Res

Liu F, Ye M, Pan Y, Zhang Y, Bian Y, Sun Z, Zhu J, Cheng K and Zou H. Integration of cell lysis, protein extraction, and digestion into one step for ultrafast sample preparation for phosphoproteome analysis. (2014) Anal Chem. 86, 6786-91 Pubmed Anal Chem

Liu J, Wang F, Zhu J, Mao J, Liu Z, Cheng K, Qin H and Zou H. Highly efficient N-glycoproteomic sample preparation by combining C(18) and graphitized carbon adsorbents. (2014) Anal Bioanal Chem. 406, 3103-9 Pubmed Anal Bioanal Chem

Sun Z, Dong J, Zhang S, Hu Z, Cheng K, Li K, Xu B, Ye M, Nie Y, Fan D and Zou H. Identification of chemoresistance-related cell-surface glycoproteins in leukemia cells and functional validation of candidate glycoproteins. (2014) J Proteome Res. 13, 1593-601 Pubmed J Proteome Res

Zhu J, Sun Z, Cheng K, Chen R, Ye M, Xu B, Sun D, Wang L, Liu J, Wang F and Zou H. Comprehensive mapping of protein N-glycosylation in human liver by combining hydrophilic interaction chromatography and hydrazide chemistry. (2014) J Proteome Res. 13, 1713-21 Pubmed J Proteome Res

Ye M, Pan Y, Cheng K and Zou H. Protein digestion priority is independent of protein abundances. (2014) Nat Methods. 11, 220-2 Pubmed Nat Methods

Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M and Zou H. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (2014) J Proteomics. 96, 253-62 Pubmed J Proteomics

Pan Y, Ye M, Zheng H, Cheng K, Sun Z, Liu F, Liu J, Wang K, Qin H and Zou H. Trypsin-catalyzed N-terminal labeling of peptides with stable isotope-coded affinity tags for proteome analysis. (2014) Anal Chem. 86, 1170-7 Pubmed Anal Chem

Song C, Wang F, Cheng K, Wei X, Bian Y, Wang K, Tan Y, Wang H, Ye M and Zou H. Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. (2014) J Proteome Res. 13, 241-8 Pubmed J Proteome Res

Bian Y, Ye M, Wang C, Cheng K, Song C, Dong M, Pan Y, Qin H and Zou H. Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow. (2013) Sci Rep. 3, 3460 Pubmed Sci Rep PMC Article

Zhang Y, Hu Z, Qin H, Liu F, Cheng K, Wu R and Zou H. Cell nucleus targeting for living cell extraction of nucleic acid associated proteins with intracellular nanoprobes of magnetic carbon nanotubes. (2013) Anal Chem. 85, 7038-43 Pubmed Anal Chem

Wang C, Ye M, Bian Y, Liu F, Cheng K, Dong M, Dong J and Zou H. Determination of CK2 specificity and substrates by proteome-derived peptide libraries. (2013) J Proteome Res. 12, 3813-21 Pubmed J Proteome Res

Pan Y, Ye M, Zhao L, Cheng K, Dong M, Song C, Qin H, Wang F and Zou H. N-terminal labeling of peptides by trypsin-catalyzed ligation for quantitative proteomics. (2013) Angew Chem Int Ed Engl. 52, 9205-9 Pubmed Angew Chem Int Ed Engl

Liu F, Ye M, Wang C, Hu Z, Zhang Y, Qin H, Cheng K and Zou H. Polyacrylamide gel with switchable trypsin activity for analysis of proteins. (2013) Anal Chem. 85, 7024-8 Pubmed Anal Chem

Zhu J, Wang F, Cheng K, Dong J, Sun D, Chen R, Wang L, Ye M and Zou H. A simple integrated system for rapid analysis of sialic-acid-containing N-glycopeptides from human serum. (2013) Proteomics. 13, 1306-13 Pubmed Proteomics

Liu J, Wang F, Lin H, Zhu J, Bian Y, Cheng K and Zou H. Monolithic capillary column based glycoproteomic reactor for high-sensitive analysis of N-glycoproteome. (2013) Anal Chem. 85, 2847-52 Pubmed Anal Chem

Wang X, Bian Y, Cheng K, Gu LF, Ye M, Zou H, Sun SS and He JX. A large-scale protein phosphorylation analysis reveals novel phosphorylation motifs and phosphoregulatory networks in Arabidopsis. (2013) J Proteomics. 78, 486-98 Pubmed J Proteomics

Zhang Y, Hu Z, Qin H, Wei X, Cheng K, Liu F, Wu R and Zou H. Highly efficient extraction of cellular nucleic acid associated proteins in vitro with magnetic oxidized carbon nanotubes. (2012) Anal Chem. 84, 10454-62 Pubmed Anal Chem

Sun Z, Chen R, Cheng K, Liu H, Qin H, Ye M and Zou H. A new method for quantitative analysis of cell surface glycoproteome. (2012) Proteomics. 12, 3328-37 Pubmed Proteomics

Sun Z, Qin H, Wang F, Cheng K, Dong M, Ye M and Zou H. Capture and dimethyl labeling of glycopeptides on hydrazide beads for quantitative glycoproteomics analysis. (2012) Anal Chem. 84, 8452-6 Pubmed Anal Chem

Dong M, Ye M, Cheng K, Song C, Pan Y, Wang C, Bian Y and Zou H. Depletion of acidic phosphopeptides by SAX to improve the coverage for the detection of basophilic kinase substrates. (2012) J Proteome Res. 11, 4673-81 Pubmed J Proteome Res

Zhu J, Wang F, Chen R, Cheng K, Xu B, Guo Z, Liang X, Ye M and Zou H. Centrifugation assisted microreactor enables facile integration of trypsin digestion, hydrophilic interaction chromatography enrichment, and on-column deglycosylation for rapid and sensitive N-glycoproteome analysis. (2012) Anal Chem. 84, 5146-53 Pubmed Anal Chem

Bian Y, Ye M, Song C, Cheng K, Wang C, Wei X, Zhu J, Chen R, Wang F and Zou H. Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach. (2012) J Proteome Res. 11, 2828-37 Pubmed J Proteome Res

Wang X, Bian Y, Cheng K, Zou H, Sun SS and He JX. A comprehensive differential proteomic study of nitrate deprivation in Arabidopsis reveals complex regulatory networks of plant nitrogen responses. (2012) J Proteome Res. 11, 2301-15 Pubmed J Proteome Res

Zhang M, Han G, Wang C, Cheng K, Li R, Liu H, Wei X, Ye M and Zou H. A bead-based approach for large-scale identification of in vitro kinase substrates. (2011) Proteomics. 11, 4632-7 Pubmed Proteomics

Wang F, Song C, Cheng K, Jiang X, Ye M and Zou H. Perspectives of comprehensive phosphoproteome analysis using shotgun strategy. (2011) Anal Chem. 83, 8078-85 Pubmed Anal Chem

Wang C, Ye M, Han G, Chen R, Zhang M, Jiang X, Cheng K, Wang F and Zou H. Enrichment of peptides containing consensus sequence by an enzymatic approach for targeted analysis of proteins. (2011) Proteomics. 11, 3578-81 Pubmed Proteomics

Zhang M, Wang C, Bian Y, Cheng K, Wei X, Ye M and Zou H. [Proteomic peptide library for determination of substrate motif of casein kinase 2]. (2011) Se Pu. 29, 706-11 Pubmed Se Pu

Jiang Y, Liu H, Li H, Wang F, Cheng K, Zhou G, Zhang W, Ye M, Cao Y, Liu W and Zou H. A proteomic analysis of engineered tendon formation under dynamic mechanical loading in vitro. (2011) Biomaterials. 32, 4085-95 Pubmed Biomaterials

Jiang X, Ye M, Cheng K and Zou H. ArMone: a software suite specially designed for processing and analysis of phosphoproteome data. (2010) J Proteome Res. 9, 2743-51 Pubmed J Proteome Res

Wei S, Bian Y, Zhao Q, Chen S, Mao J, Song C, Cheng K, Xiao Z, Zhang C, Ma W, Zou H, Ye M and Dai S. Salinity-Induced Palmella Formation Mechanism in Halotolerant Algae Revealed by Quantitative Proteomics and Phosphoproteomics. (2017) Front Plant Sci. 8, 810 Pubmed Front Plant Sci PMC Article

Sun Z, Sun D, Wang F, Cheng K, Zhang Z, Xu B, Ye M, Wang L and Zou H. Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling. (2014) Clin Proteomics. 11, 26 Pubmed Clin Proteomics PMC Article

Wang F, Cheng K, Wei X, Qin H, Chen R, Liu J and Zou H. A six-plex proteome quantification strategy reveals the dynamics of protein turnover. (2013) Sci Rep. 3, 1827 Pubmed Sci Rep PMC Article