Sample Preparation and Protein Determination for 2D-DIGE Proteomics.
Difference gel electrophoresis
Homogenization
Protein assay
Proteomics
Top-down proteomics
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
15
11
2022
pubmed:
16
11
2022
medline:
19
11
2022
Statut:
ppublish
Résumé
Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a widely employed method for efficient protein separation and the determination of abundance changes in distinct proteoforms. This makes this gel-based method a key technique of comparative approaches in top-down proteomics. For the appropriate screening of proteome-wide alterations, initial preparative steps involve sample handling, homogenization, subcellular fractionation, and the determination of protein concentration, which makes the optimal application of these techniques a crucial part of a successful initiation of a new 2D-DIGE-based analysis. This chapter describes sample homogenization and a standardized protein assay for the preparation of homogenates with a known protein concentration for subsequent differential fluorescent tagging and two-dimensional gel electrophoretic separation.
Identifiants
pubmed: 36378448
doi: 10.1007/978-1-0716-2831-7_22
doi:
Substances chimiques
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
325-337Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Uzozie AC, Aebersold R (2018) Advancing translational research and precision medicine with targeted proteomics. J Proteome 189:1–10
doi: 10.1016/j.jprot.2018.02.021
Westermeier R (2014) Looking at proteins from two dimensions: a review on five decades of 2D electrophoresis. Arch Physiol Biochem 120:168–172
doi: 10.3109/13813455.2014.945188
pubmed: 25137570
Zhan X, Li B, Zhan X, Schlüter H, Jungblut PR, Coorssen JR (2019) Innovating the concept and practice of two-dimensional gel electrophoresis in the analysis of proteomes at the proteoform level. Proteomes 7:36
doi: 10.3390/proteomes7040036
pubmed: 31671630
pmcid: 6958347
Dowling P, Zweyer M, Swandulla D, Ohlendieck K (2019) Characterization of contractile proteins from skeletal muscle using gel-based top-down proteomics. Proteomes 7:25
doi: 10.3390/proteomes7020025
pubmed: 31226838
pmcid: 6631179
Arentz G, Weiland F, Oehler MK, Hoffmann P (2015) State of the art of 2D DIGE. Proteomics Clin Appl 9:277–288
doi: 10.1002/prca.201400119
pubmed: 25400138
Timms JF, Cramer R (2008) Difference gel electrophoresis. Proteomics 8:4886–4897
doi: 10.1002/pmic.200800298
pubmed: 19003860
Minden JS, Dowd SR, Meyer HE, Stühler K (2009) Difference gel electrophoresis. Electrophoresis 30:S156–S161
doi: 10.1002/elps.200900098
pubmed: 19517495
Kondo T (2019) Cancer biomarker development and two-dimensional difference gel electrophoresis (2D-DIGE). Biochim Biophys Acta Proteins Proteomics 1867:2–8
doi: 10.1016/j.bbapap.2018.07.002
pubmed: 30392560
Carberry S, Zweyer M, Swandulla D, Ohlendieck K (2013) Application of fluorescence two-dimensional difference in-gel electrophoresis as a proteomic biomarker discovery tool in muscular dystrophy research. Biology (Basel) 2:1438–1464
Magagnotti C, Fermo I, Carletti RM, Ferrari M, Bachi A (2010) Comparison of different depletion strategies for improving resolution of the human urine proteome. Clin Chem Lab Med 48:531–535
doi: 10.1515/CCLM.2010.109
pubmed: 20148726
Zhang AH, Sun H, Yan GL, Han Y, Wang XJ (2013) Serum proteomics in biomedical research: a systematic review. Appl Biochem Biotechnol 170:774–786
doi: 10.1007/s12010-013-0238-7
pubmed: 23609910
Simpson RJ (2010) Homogenization of mammalian tissue. Cold Spring Harb Protoc 2010:pdb.prot5455
DeCaprio J, Kohl TO (2019) Using dounce homogenization to lyse cells for immunoprecipitation. Cold Spring Harb Protoc 2019(7):pdb-rot098574
doi: 10.1101/pdb.prot098574
Dias PRF, Gandra PG, Brenzikofer R, Macedo DV (2020) Subcellular fractionation of frozen skeletal muscle samples. Biochem Cell Biol 98:293–298
doi: 10.1139/bcb-2019-0219
pubmed: 31608669
Goldberg S (2021) Mechanical/physical methods of cell disruption and tissue homogenization. Methods Mol Biol 2261:563–585
doi: 10.1007/978-1-0716-1186-9_36
pubmed: 33421015
Lee YH, Tan HT, Chung MC (2010) Subcellular fractionation methods and strategies for proteomics. Proteomics 10:3935–3956
doi: 10.1002/pmic.201000289
pubmed: 21080488
Zhang H, Lyden D (2019) Asymmetric-flow field-flow fractionation technology for exomere and small extracellular vesicle separation and characterization. Nat Protoc 14:1027–1053
doi: 10.1038/s41596-019-0126-x
pubmed: 30833697
pmcid: 6733524
Jalaludin I, Lubman DM, Kim J (2021) A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery. Mass Spectrom Rev 8:e21749
Noble JE, Bailey MJ (2009) Quantitation of protein. Methods Enzymol 463:73–95
doi: 10.1016/S0076-6879(09)63008-1
pubmed: 19892168
Goldring JPD (2019) Measuring protein concentration with absorbance, Lowry, Bradford Coomassie blue, or the Smith bicinchoninic acid assay before electrophoresis. Methods Mol Biol 1855:31–39
doi: 10.1007/978-1-4939-8793-1_3
pubmed: 30426404
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
doi: 10.1016/0003-2697(76)90527-3
pubmed: 942051
Georgiou CD, Grintzalis K, Zervoudakis G, Papapostolou I (2008) Mechanism of Coomassie brilliant blue G-250 binding to proteins: a hydrophobic assay for nanogram quantities of proteins. Anal Bioanal Chem 391:391–403
doi: 10.1007/s00216-008-1996-x
pubmed: 18327568
Walker JM (1994) The bicinchoninic acid (BCA) assay for protein quantitation. Methods Mol Biol 32:5–8
pubmed: 7951748
Waheed AA, Rao KS, Gupta PD (2000) Mechanism of dye binding in the protein assay using eosin dyes. Anal Biochem 287:73–79
doi: 10.1006/abio.2000.4793
pubmed: 11078585
Zheng H, Mao YX, Li DH, Zhu CQ (2003) Dye-binding protein assay using a long-wave-absorbing cyanine probe. Anal Biochem 318:86–90
doi: 10.1016/S0003-2697(03)00163-5
pubmed: 12782035
Wilkinson-White LE, Easterbrook-Smith SB (2008) A dye-binding assay for measurement of the binding of Cu(II) to proteins. J Inorg Biochem 102:1831–1838
doi: 10.1016/j.jinorgbio.2008.06.008
pubmed: 18657322
Antharavally BS, Mallia KA, Rangaraj P, Haney P, Bell PA (2009) Quantitation of proteins using a dye-metal-based colorimetric protein assay. Anal Biochem 385:342–345
doi: 10.1016/j.ab.2008.11.024
pubmed: 19084494
Shen YX, Xiao K, Liang P, Ma YW, Huang X (2013) Improvement on the modified Lowry method against interference of divalent cations in soluble protein measurement. Appl Microbiol Biotechnol 97:4167–4178
doi: 10.1007/s00253-013-4783-3
pubmed: 23474613
Snider EJ, Crowley AR, Raykin J, Kim RK, Splaine F, Ethier CR (2020) A flexible, robust microbead-based assay for quantification and normalization of target protein concentrations. Anal Biochem 590:113510
doi: 10.1016/j.ab.2019.113510
pubmed: 31758924
May C, Serschnitzki B, Marcus K (2021) Good old-fashioned protein concentration determination by amino acid analysis. Methods Mol Biol 2228:21–28
doi: 10.1007/978-1-0716-1024-4_2
pubmed: 33950480