Recent Advances in Proteomics

doi:10.11944/j.issn.1000-0518.2018.09.180208

Chinese Journal of Applied Chemistry ›› 2018, Vol. 35 ›› Issue (9): 977-983.DOI: 10.11944/j.issn.1000-0518.2018.09.180208

• Review • Previous Articles Next Articles

Recent Advances in Proteomics

ZHAO Qun,ZHANG Lihua(),ZHANG Yukui

CAS Key Laboratory of Separation Science for Analytical Chemistry,Dalian Institute of Chemical Physics,Chinese Academy of Sciences,Dalian,Liaoning 116023,China

Received:2018-06-07 Accepted:2018-06-09 Published:2018-09-01 Online:2018-08-06
Contact: ZHANG Lihua
Supported by:
Supported by the China State Key Basic Research Program Grants(No.2017YFA0505003), the National Natural Science Foundation of China(No.21775150, No.21505136)

Abstract

Abstract:

Proteomics, as one of the foremost branches of science in the post-genome era, is mainly focused on the expression, translational modification and interaction of proteins in cells, tissues and organs. With the rapid advancement of precision medicine and life science, higher and higher requirements have been put forward for the development of analytical methods for proteomics. Herein, we summarized the new technologies for proteome research since 2013 and prospected the future of new technics and methods for protein research.

Key words: proteome, sample preparation, protein quantification, protein-protein interaction

ZHAO Qun,ZHANG Lihua,ZHANG Yukui. Recent Advances in Proteomics[J]. Chinese Journal of Applied Chemistry, 2018, 35(9): 977-983.

References

[1]	Wolters D,Washburn M,Yates J R.An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics[J]. Anal Chem,2001,73(23):5683-5690.
[2]	Hebert A,Richards A,Bailey D,et al. The One Hour Yeast Proteome[J]. Mol Cell Proteomics,2014,13(1):339-347.
[3]	Kelstrup C,Jersie-Christensen R,Batth T,et al. 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.
[4]	Ding C,Jiang J,Wei J,et al. A Fast Workflow for Identification and Quantification of Proteomes[J]. Mol Cell Proteomics,2013,12(8):2370-2380.
[5]	Zhao Q,Fang F,Liang Y,et al. 1-Dodecyl-3-Methylimidazolium Chloride-Assisted Sample Preparation Method for Efficient Integral Membrane Proteome Analysis[J]. Anal Chem,2014,86(15):7544-7550.
[6]	Zhao Q,Fang F,Shan Y,et al. In-Depth Proteome Coverage by Improving Efficiency for Membrane Proteome Analysis[J]. Anal Chem,2017,89(10):5179-5185.
[7]	Liu J,Wang F,Mao J,et al. 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.
[8]	Li Z,Huang M,Wang X,et al. Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis[J]. Anal Chem,2018,90(8):5430-5438.
[9]	Zhu Y,Piehowski P,Zhao R,et al. Nanodroplet Processing Platform for Deep and Quantitative Proteome Profiling of 10~100 Mammalian Cells[J]. Nat Commun,2018,9(1):882-892.
[10]	Zhu Y,Clair G,Chrisler W,et al. Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS[J]. Angew Chem Int Ed Engl,2018,DOI:
[11]	Yuan H,Zhang S,Zhao B,et al. Enzymatic Reactor with Trypsin Immobilized on Graphene Oxide Modified Polymer Microspheres to Achieve Automated Proteome Quantification[J]. Anal Chem,2017,89(12):6324-6329.
[12]	Zhang X,Zhu S,Xiong Y,et al. 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.
[13]	Fan C,Shi Z,Pan Y,et al. 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.
[14]	Piovesana S,Capriotti A,Cavaliere C,et al. New Magnetic Graphitized Carbon Black TiO2 Composite for Phosphopeptide Selective Enrichment in Shotgun Phosphoproteomics[J]. Anal Chem,2016,88(24):12043-12050.
[15]	Hwang L,Ayaz-Guner S,Gregorich Z,et al. Specific Enrichment of Phosphoproteins Using Functionalized Multivalent Nanoparticles[J]. J Am Chem Soc,2015,137(7):2432-2435.
[16]	Zhou H,Ye M,Dong J,et al. Mohammed S. Robust Phosphoproteome Enrichment Using Monodisperse Microsphere-Based Immobilized Titanium(Ⅳ) Ion Affinity Chromatography[J]. Nat Protoc,2013,8(3):461-480.
[17]	Bian Y,Li L,Dong M,et al. Ultra-Deep Tyrosine Phosphoproteomics Enabled by a Phosphotyrosine Superbinder[J]. Nat Chem Biol,2016,12(11):959-968.
[18]	Li Y,Wang Y,Dong M,et al. 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.
[19]	Zhu J,Sun Z,Cheng K,et al. 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.
[20]	Dong X,Qin H,Mao J,et al. 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.
[21]	Liu J,Yang K,Shao W,et al. 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.
[22]	Zhang W,Liu T,Dong H,et al. 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.
[23]	Ordureau A,Munch C,Harper J.Quantifying Ubiquitin Signaling[J]. Mol Cell,2015,58(4): 660-676.
[24]	Beaudette P,Popp O,Dittmar G.Proteomic Techniques to Probe the Ubiquitin Landscape[J]. Proteomics,2016,16(2):273-287.
[25]	Gao Y,Li Y,Zhang C,et al. Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains(ThUBDs)[J]. Mol Cell Proteomics,2016,15(4):1381-1396.
[26]	Rardin M,Newman J,Held J,et al. 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.
[27]	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.
[28]	Yang X,Dong X,Zhang K,et al. A Molecularly Imprinted Polymer as an Antibody Mimic with Affinity for Lysine Acetylated Peptides[J]. J Mat Chem B,2016,4(5):920-928.
[29]	Garnett G,Starke M,Shaurya A,et al. Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics[J]. Anal Chem,2016,88(7):3697-3703.
[30]	Zhang Y,Liu W,Sohai M,et al. Enzymatic Allylation of Catechols[J]. Chem Lett,2015,44(7):949-951.
[31]	Yan J,Guo C,Liu X,et al. A Simple and Highly Stable Free-flow Electrophoresis Device with Thermoelectric Cooling System[J]. J Chromatogr A,2013,1321:119-126.
[32]	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.
[33]	Wunsch B,Smith J,Gifford S,et al. Nanoscale Lateral Displacement Arrays for the Separation of Exosomes and Colloids Down to 20 nm[J]. Nat Nanotechnol,2016,11:936-940.
[34]	Battle K,Jackson J,Witek M,et al. Solid-phase Extraction and Purification of Membrane Proteins Using a UV-modified PMMA Microfluidic Bioaffinity μSPE Device[J]. Analyst,2014,139(6):1355-1363.
[35]	Fang F,Zhao Q,Li X,et al. Dissolving Capability Difference Based Sequential Extraction:A Versatile Tool for In-depth Membrane Proteome Analysis[J]. Anal Chim Acta,2016,945:39-46.
[36]	Weng Y,Sui Z,Shan Y,et al. Effective Isolation of Exosomes with Polyethylene Glycol from Cell Culture Supernatant for In-depth Proteome Profiling[J]. Analyst,2016,141(15):4640-4646.
[37]	Weng Y,Qu Y,Jiang H,et al. 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.
[38]	Chen Q,Yan G,Gao M,et al. 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.
[39]	Liu F,Ye M,Pan Y,et al. 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.
[40]	Kim M,Pinto S,Getnet D,et al. A Draft Map of the Human Proteome[J]. Nature,2014,509(7502):575-581.
[41]	Wilhelm M,Schlegl J,Hahne H,et al. Mass-spectrometry-based Draft of the Human Proteome[J]. Nature,2014,509(7502):582-587.
[42]	Uhlen M,Fagerberg L,Hallstroem B,et al. Tissue-based Map of the Human Proteome[J]. Science,2015,347(6220):394-404.
[43]	Chen Y,Li Y,Zhong J,et al. 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.
[44]	Chen L,Zhai L,Li Y,et al. Development of Gel-Filter Method for High Enrichment of Low-Molecular Weight Proteins from Serum[J]. PLoS One,2015,10(2):e0115862.
[45]	Ding C,Chan D,Liu W,et al. 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.
[46]	Meier F,Geyer P,Virreira Winter S,et al. BoxCar Acquisition Method Enables Single-shot Proteomics at a Depth of 10,000 Proteins in 100 Minutes[J]. Nat Methods,2018,DOI:
[47]	Zhou Y,Shan Y,Wu Q,et al. Mass Defect-based Pseudo-isobaric Dimethyl Labeling for Proteome Quantification[J]. Anal Chem,2013,85(22):10658-10663.
[48]	Di Y,Zhang Y,Zhang L,et al. MdFDIA:A Mass Defect Based Four-Plex Data-Independent Acquisition Strategy for Proteome Quantification[J]. Anal Chem,2017,89(19):10248-10255.
[49]	Tan D,Li Q,Zhang M,et al. Trifunctional Cross-linker for Mapping Protein-protein Interaction Networks and Comparing Protein Conformational States[J]. eLife,2016,DOI:
[50]	Ding Y,Fan S,Li S,et al. 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.
[51]	Liu F,Rijkers D,Post H,et al. Proteome-wide Profiling of Protein Assemblies by Cross-linking Mass Spectrometry[J]. Nat Method,2015,12(12):1179-1184.
[52]	Wu X,Chavez J,Schweppe D,et al. In Vivo Protein Interaction Network Analysis Reveals Porin-localized Antibiotic Inactivation in Acinetobacter Baumannii Strain AB5075[J]. Nat Commun,2016,7:13414-13427.
[53]	Chi H,He K,Yang B,et al. 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.
[54]	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.
[55]	Zhang S,Wu Q,Shan Y,et al. 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.
[56]	Liu M,Zeng W,Fang P,et al. 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.
[57]	Tyanova S,Temu T,Cox J.The MaxQuant Computational Platform for Mass Spectrometry-based Shotgun Proteomics[J]. Nat Protoc,2016,11(12):2301-2319.
[58]	Liu C,Song C,Yuan Z,et al. pQuant Improves Quantitation by Keeping Out Interfering Signals and Evaluating the Accuracy of Calculated Ratios[J]. Anal Chem,2014,86(11):5286-5294.
[59]	Chang C,Zhang J,Han M,et al. SILVER: An Efficient Tool for Stable Isotope Labeling LC-MS Data Quantitative Analysis with Quality Control Methods[J]. Bioinformatics,2014,30(4):586-587.

Recent Advances in Proteomics

RichHTML

PDF

Knowledge

Cited

Abstract

Cite this article

share this article

References

Related Articles 0

Recommended Articles

Metrics

Comments