Recent Advances in Proteomics
- Corresponding author: ZHANG Lihua, lihuazhang@dicp.ac.cn
Citation:
ZHAO Qun, ZHANG Lihua, ZHANG Yukui. Recent Advances in Proteomics[J]. Chinese Journal of Applied Chemistry,
;2018, 35(9): 977-983.
doi:
10.11944/j.issn.1000-0518.2018.09.180208
Wolters D, Washburn M, Yates J R. An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics[J]. Anal Chem, 2001,73(23):5683-5690. doi: 10.1021/ac010617e
Hebert A, Richards A, Bailey D. The One Hour Yeast Proteome[J]. Mol Cell Proteomics, 2014,13(1):339-347. doi: 10.1074/mcp.M113.034769
Kelstrup C, Jersie-Christensen R, Batth T. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer[J]. J Proteome Res, 2014,13(12):6187-6195. doi: 10.1021/pr500985w
Ding C, Jiang J, Wei J. A Fast Workflow for Identification and Quantification of Proteomes[J]. Mol Cell Proteomics, 2013,12(8):2370-2380. doi: 10.1074/mcp.O112.025023
Zhao Q, Fang F, Liang Y. 1-Dodecyl-3-Methylimidazolium Chloride-Assisted Sample Preparation Method for Efficient Integral Membrane Proteome Analysis[J]. Anal Chem, 2014,86(15):7544-7550. doi: 10.1021/ac5013267
Zhao Q, Fang F, Shan Y. In-Depth Proteome Coverage by Improving Efficiency for Membrane Proteome Analysis[J]. Anal Chem, 2017,89(10):5179-5185. doi: 10.1021/acs.analchem.6b04232
Liu J, Wang F, Mao J. High-Sensitivity N-Glycoproteomic Analysis of Mouse Brain Tissue by Protein Extraction with a Mild Detergent of N-Dodecyl β-D-Maltoside[J]. Anal Chem, 2015,87(4):2054-2057. doi: 10.1021/ac504700t
Li Z, Huang M, Wang X. Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis[J]. Anal Chem, 2018,90(8):5430-5438. doi: 10.1021/acs.analchem.8b00661
Zhu Y, Piehowski P, Zhao R. Nanodroplet Processing Platform for Deep and Quantitative Proteome Profiling of 10~100 Mammalian Cells[J]. Nat Commun, 2018,9(1):882-892. doi: 10.1038/s41467-018-03367-w
Zhu Y, Clair G, Chrisler W. Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS[J]. Angew Chem Int Ed Engl, 2018. doi: 10.1002/ange.201802843
Yuan H, Zhang S, Zhao B. Enzymatic Reactor with Trypsin Immobilized on Graphene Oxide Modified Polymer Microspheres to Achieve Automated Proteome Quantification[J]. Anal Chem, 2017,89(12):6324-6329. doi: 10.1021/acs.analchem.7b00682
Zhang X, Zhu S, Xiong Y. Development of a MALDI-TOF MS Strategy for the High-Throughput Analysis of Biomarkers:On-Target Aptamer Immobilization and Laser-Accelerated Proteolysis[J]. Angew Chem Int Ed, 2013,52(23):6055-6058. doi: 10.1002/anie.201300566
Fan C, Shi Z, Pan Y. Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage[J]. Anal Chem, 2014,86(3):1452-1458. doi: 10.1021/ac402696b
Piovesana S, Capriotti A, Cavaliere C. New Magnetic Graphitized Carbon Black TiO2 Composite for Phosphopeptide Selective Enrichment in Shotgun Phosphoproteomics[J]. Anal Chem, 2016,88(24):12043-12050. doi: 10.1021/acs.analchem.6b02345
Hwang L, Ayaz-Guner S, Gregorich Z. Specific Enrichment of Phosphoproteins Using Functionalized Multivalent Nanoparticles[J]. J Am Chem Soc, 2015,137(7):2432-2435. doi: 10.1021/ja511833y
Zhou H, Ye M, Dong J. Mohammed S. Robust Phosphoproteome Enrichment Using Monodisperse Microsphere-Based Immobilized Titanium(Ⅳ) Ion Affinity Chromatography[J]. Nat Protoc, 2013,8(3):461-480. doi: 10.1038/nprot.2013.010
Bian Y, Li L, Dong M. Ultra-Deep Tyrosine Phosphoproteomics Enabled by a Phosphotyrosine Superbinder[J]. Nat Chem Biol, 2016,12(11):959-968. doi: 10.1038/nchembio.2178
Li Y, Wang Y, Dong M. Sensitive Approaches for the Assay of the Global Protein Tyrosine Phosphorylation in Complex Samples Using a Mutated SH2 Domain[J]. Anal Chem, 2017,89(4):2304-2311. doi: 10.1021/acs.analchem.6b03812
Zhu J, Sun Z, Cheng K. Comprehensive Mapping of Protein N-Glycosylation in Human Liver by Combining Hydrophilic Interaction Chromatography and Hydrazide Chemistry[J]. J Proteome Res, 2014,13(3):1713-1721. doi: 10.1021/pr401200h
Dong X, Qin H, Mao J. In-Depth Analysis of Glycoprotein Sialylation in Serum Using a Dual-Functional Material with Superior Hydrophilicity and Switchable Surface Charge[J]. Anal Chem, 2017,89(7):3966-3972. doi: 10.1021/acs.analchem.6b04394
Liu J, Yang K, Shao W. Boronic Acid-Functionalized Particles with Flexible Three-Dimensional Polymer Branch for Highly Specific Recognition of Glycoproteins[J]. ACS Appl Mater Interfaces, 2016,8(15):9552-9556. doi: 10.1021/acsami.6b01829
Zhang W, Liu T, Dong H. Synthesis of a Highly Azide-Reactive and Thermosensitive Biofunctional Reagent for Efficient Enrichment and Large-Scale Identification of O-GlcNAc Proteins by Mass Spectrometry[J]. Anal Chem, 2017,89(11):5810-5817. doi: 10.1021/acs.analchem.6b04960
Ordureau A, Munch C, Harper J. Quantifying Ubiquitin Signaling[J]. Mol Cell, 2015,58(4):660-676. doi: 10.1016/j.molcel.2015.02.020
Beaudette P, Popp O, Dittmar G. Proteomic Techniques to Probe the Ubiquitin Landscape[J]. Proteomics, 2016,16(2):273-287. doi: 10.1002/pmic.201500290
Gao Y, Li Y, Zhang C. Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains(ThUBDs)[J]. Mol Cell Proteomics, 2016,15(4):1381-1396. doi: 10.1074/mcp.O115.051839
Rardin M, Newman J, Held J. Label-free Quantitative Proteomics of the Lysine Acetylome in Mitochondria Identifies Substrates of SIRT3 in Metabolic Pathways[J]. Proc Natl Acad Sci, 2013,110(16):6601-6606. doi: 10.1073/pnas.1302961110
Li L, Yan G, Zhang X. Isolation of Acetylated and Free N-Terminal Peptides from Proteomic Samples Based on Tresyl-Functionalized Microspheres[J]. Talanta, 2015,144:122-128. doi: 10.1016/j.talanta.2015.05.068
Yang X, Dong X, Zhang K. A Molecularly Imprinted Polymer as an Antibody Mimic with Affinity for Lysine Acetylated Peptides[J]. J Mat Chem B, 2016,4(5):920-928. doi: 10.1039/C5TB02620B
Garnett G, Starke M, Shaurya A. Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics[J]. Anal Chem, 2016,88(7):3697-3703. doi: 10.1021/acs.analchem.5b04508
Zhang Y, Liu W, Sohai M. Enzymatic Allylation of Catechols[J]. Chem Lett, 2015,44(7):949-951. doi: 10.1246/cl.150237
Yan J, Guo C, Liu X. A Simple and Highly Stable Free-flow Electrophoresis Device with Thermoelectric Cooling System[J]. J Chromatogr A, 2013,1321:119-126. doi: 10.1016/j.chroma.2013.10.058
Yang J, Lee J, Moon M. High Speed Size Sorting of Subcellular Organelles by Flow Field-Flow Fractionation[J]. Anal Chem, 2015,87(12):6342-6348. doi: 10.1021/acs.analchem.5b01207
Wunsch B, Smith J, Gifford S. Nanoscale Lateral Displacement Arrays for the Separation of Exosomes and Colloids Down to 20 nm[J]. Nat Nanotechnol, 2016,11:936-940. doi: 10.1038/nnano.2016.134
Battle K, Jackson J, Witek M. Solid-phase Extraction and Purification of Membrane Proteins Using a UV-modified PMMA Microfluidic Bioaffinity μSPE Device[J]. Analyst, 2014,139(6):1355-1363. doi: 10.1039/C3AN02400H
Fang F, Zhao Q, Li X. Dissolving Capability Difference Based Sequential Extraction:A Versatile Tool for In-depth Membrane Proteome Analysis[J]. Anal Chim Acta, 2016,945:39-46. doi: 10.1016/j.aca.2016.09.032
Weng Y, Sui Z, Shan Y. Effective Isolation of Exosomes with Polyethylene Glycol from Cell Culture Supernatant for In-depth Proteome Profiling[J]. Analyst, 2016,141(15):4640-4646. doi: 10.1039/C6AN00892E
Weng Y, Qu Y, Jiang H. An Integrated Sample Pretreatment Platform for Quantitative N-Glycoproteome Analysis with Combination of On-line Glycopeptide Enrichment, Deglycosylation and Dimethyl Labeling[J]. Anal Chim Acta, 2014,833:1-8. doi: 10.1016/j.aca.2014.04.037
Chen Q, Yan G, Gao M. Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis[J]. Anal Chem, 2015,87(13):6674-6680. doi: 10.1021/acs.analchem.5b00808
Liu F, Ye M, Pan Y. Integration of Cell Lysis, Protein Extraction, and Digestion into One Step for Ultrafast Sample Preparation for Phosphoproteome Analysis[J]. Anal Chem, 2014,86(14):6786-6791. doi: 10.1021/ac5002146
Kim M, Pinto S, Getnet D. A Draft Map of the Human Proteome[J]. Nature, 2014,509(7502):575-581. doi: 10.1038/nature13302
Wilhelm M, Schlegl J, Hahne H. Mass-spectrometry-based Draft of the Human Proteome[J]. Nature, 2014,509(7502):582-587. doi: 10.1038/nature13319
Uhlen M, Fagerberg L, Hallstroem B. Tissue-based Map of the Human Proteome[J]. Science, 2015,347(6220):394-404.
Chen Y, Li Y, Zhong J. Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins[J]. J Proteome Res, 2015,14(9):3693-3709. doi: 10.1021/pr501103r
Chen L, Zhai L, Li Y. Development of Gel-Filter Method for High Enrichment of Low-Molecular Weight Proteins from Serum[J]. PLoS One, 2015,10(2)e0115862. doi: 10.1371/journal.pone.0115862
Ding C, Chan D, Liu W. Proteome-wide Profiling of Activated Transcription Factors with a Concatenated Tandem Array of Transcription Factor Response Elements[J]. Proc Natl Acad Sci, 2013,110(17):6771-6776. doi: 10.1073/pnas.1217657110
Meier F, Geyer P, Virreira Winter S. BoxCar Acquisition Method Enables Single-shot Proteomics at a Depth of 10, 000 Proteins in 100 Minutes[J]. Nat Methods, 2018. doi: 10.1038/s41592-018-0003-5
Zhou Y, Shan Y, Wu Q. Mass Defect-based Pseudo-isobaric Dimethyl Labeling for Proteome Quantification[J]. Anal Chem, 2013,85(22):10658-10663. doi: 10.1021/ac402834w
Di Y, Zhang Y, Zhang L. MdFDIA:A Mass Defect Based Four-Plex Data-Independent Acquisition Strategy for Proteome Quantification[J]. Anal Chem, 2017,89(19):10248-10255. doi: 10.1021/acs.analchem.7b01635
Tan D, Li Q, Zhang M. Trifunctional Cross-linker for Mapping Protein-protein Interaction Networks and Comparing Protein Conformational States[J]. eLife, 2016. doi: 10.7554/eLife.12509
Ding Y, Fan S, Li S. Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes Through the Use of Multiple Cross-Linkers[J]. Anal Chem, 2016,88(8):4461-4469. doi: 10.1021/acs.analchem.6b00281
Liu F, Rijkers D, Post H. Proteome-wide Profiling of Protein Assemblies by Cross-linking Mass Spectrometry[J]. Nat Method, 2015,12(12):1179-1184. doi: 10.1038/nmeth.3603
Wu X, Chavez J, Schweppe D. In Vivo Protein Interaction Network Analysis Reveals Porin-localized Antibiotic Inactivation in Acinetobacter Baumannii Strain AB5075[J]. Nat Commun, 2016,7:13414-13427. doi: 10.1038/ncomms13414
Chi H, He K, Yang B. pFind-Alioth:A Novel Unrestricted Database Search Algorithm to Improve the Interpretation of High-resolution MS/MS Data[J]. J Proteomics, 2015,125:89-97. doi: 10.1016/j.jprot.2015.05.009
Wenger C, Coon J. A Proteomics Search Algorithm Specifically Designed for High-resolution Tandem Mass Spectra[J]. J Proteome Res, 2013,12(3):1377-1386. doi: 10.1021/pr301024c
Zhang S, Wu Q, Shan Y. A Paired Ions Scoring Algorithm Based on Morpheus for Simultaneous Identification and Quantification of Proteome Samples Prepared by Isobaric Peptide Termini Labeling Strategies[J]. Proteomics, 2015,15(11):1781-8. doi: 10.1002/pmic.v15.11
Liu M, Zeng W, Fang P. pGlyco 2.0 Enables Precision N-Glycoproteomics with Comprehensive Quality Control and One-step Mass Spectrometry for Intact Glycopeptide Identification[J]. Nat Commun, 2017,8(1):438-451. doi: 10.1038/s41467-017-00535-2
Tyanova S, Temu T, Cox J. The MaxQuant Computational Platform for Mass Spectrometry-based Shotgun Proteomics[J]. Nat Protoc, 2016,11(12):2301-2319. doi: 10.1038/nprot.2016.136
Liu C, Song C, Yuan Z. pQuant Improves Quantitation by Keeping Out Interfering Signals and Evaluating the Accuracy of Calculated Ratios[J]. Anal Chem, 2014,86(11):5286-5294. doi: 10.1021/ac404246w
Chang C, Zhang J, Han M. SILVER:An Efficient Tool for Stable Isotope Labeling LC-MS Data Quantitative Analysis with Quality Control Methods[J]. Bioinformatics, 2014,30(4):586-587. doi: 10.1093/bioinformatics/btt726
Wei Peng , Baoying Wen , Huamin Li , Yiru Wang , Jianfeng Li . Exploration and Practice on Raman Scattering Spectroscopy Experimental Teaching. University Chemistry, 2024, 39(8): 230-240. doi: 10.3866/PKU.DXHX202312062
Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
Ling Bai , Limin Lu , Xiaoqiang Wang , Dongping Wu , Yansha Gao . Exploration and Practice of Teaching Reforms in “Quantitative Analytical Chemistry” under the Perspective of New Agricultural Science. University Chemistry, 2024, 39(3): 158-166. doi: 10.3866/PKU.DXHX202308101
Jiaxun Wu , Mingde Li , Li Dang . The R eaction of Metal Selenium Complexes with Olefins as a Tutorial Case Study for Analyzing Molecular Orbital Interaction Modes. University Chemistry, 2025, 40(3): 108-115. doi: 10.12461/PKU.DXHX202405098
Huiying Xu , Minghui Liang , Zhi Zhou , Hui Gao , Wei Yi . Application of Quantum Chemistry Computation and Visual Analysis in Teaching of Weak Interactions. University Chemistry, 2025, 40(3): 199-205. doi: 10.12461/PKU.DXHX202407011
Mi Wen , Baoshuo Jia , Yongqi Chai , Tong Wang , Jianbo Liu , Hailong Wu . Improvement of Fluorescence Quantitative Analysis Experiment: Simultaneous Determination of Rhodamine 6G and Rhodamine 123 in Food Using Chemometrics-Assisted Three-Dimensional Fluorescence Method. University Chemistry, 2025, 40(4): 390-398. doi: 10.12461/PKU.DXHX202405147
Hailian Tang , Siyuan Chen , Qiaoyun Liu , Guoyi Bai , Botao Qiao , Fei Liu . Stabilized Rh/hydroxyapatite Catalyst for Furfuryl Alcohol Hydrogenation: Application of Oxidative Strong Metal-Support Interactions in Reducing Conditions. Acta Physico-Chimica Sinica, 2025, 41(4): 100036-. doi: 10.3866/PKU.WHXB202408004
Yongjie ZHANG , Bintong HUANG , Yueming ZHAI . Research progress of formation mechanism and characterization techniques of protein corona on the surface of nanoparticles. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2318-2334. doi: 10.11862/CJIC.20240247
Zeyu XU , Anlei DANG , Bihua DENG , Xiaoxin ZUO , Yu LU , Ping YANG , Wenzhu YIN . Evaluation of the efficacy of graphene oxide quantum dots as an ovalbumin delivery platform and adjuvant for immune enhancement. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1065-1078. doi: 10.11862/CJIC.20240099
Min Gu , Huiwen Xiong , Liling Liu , Jilie Kong , Xueen Fang . Rapid Quantitative Detection of Procalcitonin by Microfluidics: An Instrumental Analytical Chemistry Experiment. University Chemistry, 2024, 39(4): 87-93. doi: 10.3866/PKU.DXHX202310120
Cheng Zheng , Shiying Zheng , Yanping Zhang , Shoutian Zheng , Qiaohua Wei . Synthesis, Copper Content Analysis, and Luminescent Performance Study of Binuclear Copper (I) Complexes with Isomeric Luminescence Shift: A Comprehensive Chemical Experiment Recommendation. University Chemistry, 2024, 39(7): 322-329. doi: 10.3866/PKU.DXHX202310131
Jing Wang , Pingping Li , Yuehui Wang , Yifan Xiu , Bingqian Zhang , Shuwen Wang , Hongtao Gao . Treatment and Discharge Evaluation of Phosphorus-Containing Wastewater. University Chemistry, 2024, 39(5): 52-62. doi: 10.3866/PKU.DXHX202309097
Zhaohu Li , Weidong Wang , Yuhao Liu , Mingzhe Han , Lingling Wei , Huan Jiao . Research on the Safety Management and Disposal of Chemical Laboratory Waste. University Chemistry, 2024, 39(10): 128-136. doi: 10.3866/PKU.DXHX202312090
Lisen Sun , Yongmei Hao , Zhen Huang , Yongmei Liu . Experimental Teaching Design for Viscosity Measurement Serves the Optimization of Operating Conditions for Kitchen Waste Treatment Equipment. University Chemistry, 2024, 39(2): 52-56. doi: 10.3866/PKU.DXHX202307063
Kun Xu , Xinxin Song , Zhilei Yin , Jian Yang , Qisheng Song . Comprehensive Experimental Design of Preferential Orientation of Zinc Metal by Heat Treatment for Enhanced Electrochemical Performance. University Chemistry, 2024, 39(4): 192-197. doi: 10.3866/PKU.DXHX202309050
Chunai Dai , Yongsheng Han , Luting Yan , Zhen Li , Yingze Cao . Preparation of Superhydrophobic Surfaces and Their Application in Oily Wastewater Treatment: Design of a Comprehensive Physical Chemistry Innovation Experiment. University Chemistry, 2024, 39(2): 34-40. doi: 10.3866/PKU.DXHX202307081
Zhangshu Wang , Xin Zhang , Jixin Han , Xuebing Fang , Xiufeng Zhao , Zeyu Gu , Jinjun Deng . Exploration and Design of Experimental Teaching on Ultrasonic-Enhanced Synergistic Treatment of Ternary Composite Flooding Produced Water. University Chemistry, 2024, 39(5): 116-124. doi: 10.3866/PKU.DXHX202310056
Limin Shao , Na Li . A Unified Equation Derived from the Charge Balance Equation for Constructing Acid-Base Titration Curve and Calculating Endpoint Error. University Chemistry, 2024, 39(11): 365-373. doi: 10.3866/PKU.DXHX202401086
Jia Huo , Jia Li , Yongjun Li , Yuzhi Wang . Ideological and Political Design of Physical Chemistry Teaching: Chemical Potential of Any Component in an Ideal-Dilute Solution. University Chemistry, 2024, 39(2): 14-20. doi: 10.3866/PKU.DXHX202307075
Zhuomin Zhang , Hanbing Huang , Liangqiu Lin , Jingsong Liu , Gongke Li . Course Construction of Instrumental Analysis Experiment: Surface-Enhanced Raman Spectroscopy for Rapid Detection of Edible Pigments. University Chemistry, 2024, 39(2): 133-139. doi: 10.3866/PKU.DXHX202308034