Gel electrophoresis/electroelution sorting fractionator combined with filter-aided sample preparation for deep proteomic analysis.
electroelution
electrophoresis
peptide fractionation
protein fractionation
proteomics
Journal
Journal of separation science
ISSN: 1615-9314
Titre abrégé: J Sep Sci
Pays: Germany
ID NLM: 101088554
Informations de publication
Date de publication:
May 2022
May 2022
Historique:
revised:
14
03
2022
received:
10
01
2022
accepted:
15
03
2022
pubmed:
21
3
2022
medline:
25
5
2022
entrez:
20
3
2022
Statut:
ppublish
Résumé
Sample preparation and protein fractionation are important issues for proteomic studies. Protein extraction procedures strongly affect the performance of fractionation methods by provoking protein dispersion in several fractions. The most notable exception is the gel-based electrophoretic protein fractionation due to its resolution and effectiveness of sodium dodecyl sulfate as a solubilizing agent, while its main limitation lies in the poor recovery of the gel-trapped proteins. We created a fractionator device to separate complex mixture of proteins and peptides that is based on the continuous gel electrophoresis/electroelution sorting of these molecules. In an unsupervised process, complex mixtures of proteins or peptides are fractionated into the gel while separated fractions are simultaneously and sequentially electroeluted to the solution containing wells. The performance of the device was studied for protein fractionation in terms of reproducibility, protein recovery, and loading capacity. In a setup free of sodium dodecyl sulfate, complex peptide mixtures can also be fractionated. More than 11,700 proteins were identified in the whole-cell lysate of the CaSki cell line by using the fractionator combined with the filter-aided sample preparation method and mass spectrometry analysis. Fractionator-based proteome characterization increased 1.7-fold the number of identified proteins compared to the unfractionated sample analysis.
Identifiants
pubmed: 35306742
doi: 10.1002/jssc.202100992
doi:
Substances chimiques
Peptides
0
Proteome
0
Sodium Dodecyl Sulfate
368GB5141J
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1784-1796Subventions
Organisme : The Center for Genetic Engineering and Biotechnology
Organisme : the German Ministry of Education and Science
ID : 01DN18015
Organisme : the Max-Planck Society for the Advancement of Science
Informations de copyright
© 2022 Wiley-VCH GmbH.
Références
Feist P, Hummon AB. Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples. Int J Mol Sci. 2015;16:3537-63.
Görg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004;4:3665-85.
Pomastowski P, Buszewski B. Two-dimensional gel electrophoresis in the light of new developments. Trends Anal Chem. 2014;53:167-77.
Westermeier R. Looking at proteins from two dimensions: a review on five decades of 2D electrophoresis. Arch Physiol Biochem. 2014;120:168-72.
Jiang L, He L, Fountoulakis M. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A. 2004;1023:317-20.
Antonioli P, Bachi A, Fasoli F, Righetti PG. Efficient removal of DNA from proteomic samples prior to two-dimensional map analysis. J Chromatogr A. 2009;1216:3606-12.
Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protocols. 2006;1:2856-60.
Speicher KD, Kolbas O, Harper S, Speicher DW. Systematic analysis of peptide recoveries from in-gel digestions for protein identifications in proteome studies. J Biomol Tech. 2000;11:74-86.
Yen CY, Russell S, Mendoza AM, Meyer-Arendt K, Sun S, Cios KJ, Ahn NG, Resing KA. Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra. Anal Chem. 2006;78:1071-84.
Ethier M, Hou W, Duewel HS, Figeys D. The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis. J Proteome Res. 2006;5:2754-9.
Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6:359-62.
Yu Y, Xie L, Gunawardena HP, Khatun J, Maier C, Spitzer W, Leerkes M, Giddings MC, Chen X. GOFAST: an integrated approach for efficient and comprehensive membrane proteome analysis. Anal Chem. 2012;84:9008-14.
Wiśniewski JR, Mann M. Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal Chem. 2012;84:2631-7.
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol. 2014;10:757.
Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 2014;11:319-24.
Zougman A, Selby PJ, Banks RE. Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 2014;14:1006-1000.
Batth TS, Tollenaere MAX, Ruther P, Gonzalez-Franquesa A, Prabhakar BS, Bekker-Jensen S, Deshmukh AS, Olsen JV. Protein aggregation capture on microparticles enables multipurpose proteomics sample preparation. Mol Cell Proteomics 2019;18:1027-35.
Wiśniewski JR, Zougman A, Mann M. Combination of FASP and stagetip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. Anal Biochem. 2011;410:307-9.
Kulak NA, Geyer PE, Mann M. Loss-less nano-fractionator for high sensitivity, high coverage proteomics. Mol Cell Proteomics 2017;16:694-705.
Simpson RJ, Connolly LM, Eddes JS, Pereira JJ, Moritz RL, Reid GE. Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database. Electrophoresis 2000;21:1707-32.
Lasonder E, Ishihama Y, Andersen JS, Vermunt AMW, Pain A, Sauerwein RW, Eling WMC, Hall N, Watersk AP, Stunnenberg HG Mann M. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002;419:537-42.
Ramos Y, Gutierrez E, Machado Y, Sánchez A, Castellanos-Serra L, González LJ, Fernández-de-Cossio J, Pérez-Riverol Y, Betancourt L, Gil J, Padrón G, Besada V. Proteomics based on peptide fractionation by SDS-free PAGE. J Proteome Res. 2008;7:2427-34.
Ramos Y, Besada V, Castellanos-Serra L. Peptide fractionation by SDS-free polyacrylamide gel electrophoresis for proteomic analysis via DF-PAGE. Methods Mol Biol. 2012;869:197-204.
Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, Higo D, Ishizaki J, Hasegawa H, Suzuki J, Yamashita M, Loo JA, Loo RRO, Beynon RJ, Anderson LC, Takemori N. PEPPI-MS: polyacrylamide-gel-based prefractionation for analysis of intact proteoforms and protein complexes by mass spectrometry. J Proteome Res. 2020;19:3779-91.
Kasicka V. From micro to macro: conversion of capillary electrophoretic separations of biomolecules and bioparticles to preparative free-flow electrophoresis scale. Electrophoresis 2009;30(Suppl 1):S40-52.
Foucher AL, Craft DR, Gelfand CA. Application of free flow electrophoresis to the analysis of the urine proteome. Methods Mol Biol. 2010;641:27-45.
Stastna M. Continuous flow electrophoretic separation - Recent developments and applications to biological sample analysis. Electrophoresis 2020;41:36-55.
Herbert B, Righetti PG. A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzers with isoelectric membranes. Electrophoresis 2000;21:3639-48.
Hubner NC, Ren S, Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008;8:4862-72.
Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018). J Sep Sci. 2019;42:398-414.
Chang HT, Yergey AL, Chrambach A. Electroelution of protein from bands in gel electrophoresis without gel sectioning for the purpose of protein transfer into mass spectrometry: elements of a new procedure. Electrophoresis 2001;22:394-8.
Tran JC, Doucette AA. gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal Chem. 2008;80:1568-73.
Razunguzwa TT, Biddle A, Anderson H, Zhan D, Powell M. Development of a microfluidics-based gel protein recovery system. Electrophoresis 2009;30:4020-8.
Li GQ, Shao J, Guo CG, Dong JY, Fan LY, Cao CX. A simple monolithic column electroelution for protein recovery from gel electrophoresis. Anal Biochem. 2012;430:24-31
Vellaichamy A, Tran JC, Catherman AD, Lee JE, Kellie JF, Sweet SMM, Leonid Z, Thomas PM, Ahlf DR, Durbin KR, Valaskovic GA, Kelleher NL. Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa. Anal Chem. 2009;81:6201-9.
Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolid L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nat Methods 2019;16:587-94.
Ramos Y, González A, Sosa-Acosta P, Perez-Riverol Y, García Y, Castellanos-Serra L, Gil J, Sánchez A, González LJ, Besada V. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation. J Sep Sci. 2019;42:3712-7.
Molloy MP, Herbert BR, Walsh BJ, Tyler MI, Traini M, Sánchez JC, Hochstrasser DF, Williams KL Gooley AA. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 1998;19:837-44.
Wiśniewski JR, Gaugaz FZ. Fast and sensitive total protein and peptide assays for proteomic analysis. Anal Chem. 2015;87:4110.
Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970;227:680-5.
Heukeshoven J, Dernick RJ. Improved silver staining procedure for fast staining in PhastSystem Development Unit. I. Staining of sodium dodecyl sulfate gels. Electrophoresis 1988;9:28-32.
Rappsilber J, Ishihama Y, Mann M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem. 2003;75:663-70.
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26:1367-72.
Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 2019;47(Database issue):D419-26.
Mi H, Thomas P. PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009;563:123-40.
Wiśniewski JR, Zielinska DF, Mann M. Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method. Anal Biochem. 2011;410:307-9.
Wiśniewski JR. Filter aided sample preparation: a tutorial. Anal Chim Acta 2019;1090:23-30.
Ornstein L. Disc electrophoresis. I. Background and theory. Ann NY Acad Sci. 1964;121:321.
Ramos Y, García Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V. Peptide fractionation by acid pH SDS-free electrophoresis. Electrophoresis 2011;32:1323-6
Cifuentes A, Poppe H. Behavior of peptides in capillary electrophoresis: effect of peptide charge, mass and structure. Electrophoresis 1997;18:2362-76.
Adamson NJ, Reynolds EC. Rules relating electrophoretic mobility, charge and molecular size of peptides and proteins. J Chromatogr B Biomed Sci Appl. 1997;699:133-47.
Solinova V, Kasicka V, Sazelova P, Barth T, Miksik I. Separation and investigation of structure-mobility relationship of gonadotropin-releasing hormones by capillary zone electrophoresis in conventional and isoelectric acidic background electrolytes. J Chromatogr A. 2007;1155:146-53.
Offord RE. Electrophoretic mobilities of peptides on paper and their use in the determination of amide groups. Nature 1966;211:591.
Ludwig KR, Schroll MM, Hummon AB. Comparison of in-solution, FASP, and S-trap based digestion methods for bottom-up proteomic studies. J Proteome Res. 2018;17:2480-90.
Lin LH, Chang SJ, Hu RY, Lin MW, Lin ST, Huang SH, Lyu PC, Chou HC, Lai ZY, Chuang YJ, Chan HL. Biomarker discovery for neuroendocrine cervical cancer. Electrophoresis 2014;35:2039-45.
Pan TL, Wang PW, Hung YC, Huang CH, Rau KM. Proteomic analysis reveals tanshinone IIA enhances apoptosis of advanced cervix carcinoma CaSki cells through mitochondria intrinsic and endoplasmic reticulum stress pathways. Proteomics 2013;13:3411-23.
Li X, Ran L, Fang W, Wang D. Lobaplatin arrests cell cycle progression, induces apoptosis and alters the proteome in human cervical cancer cell Line CaSki. Biomed Pharmacother. 2014;68:291-7.
Wiśniewski JR, Ostasiewicz P, Dus K, Zielinska DF, Gnad F, Mann M. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol. 2012;8:611.
Wiśniewski JR, Hein MY, Cox J, Mann MA. “Proteomic Ruler” for protein copy number and concentration estimation without spike-in standards. Mol Cell Proteomics. 2014;13:3497-506.
Nagaraj N, Wiśniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011;7:548.
Brown GC. Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells. J Theor Biol. 1991;153:195-203.
Gorodeski GL, Whittembury J. A novel fluorescence chamber for the determination of volume changes in human CaSki cell cultures attached on filters. Cell Biochem Biophys. 1998;29:307-31.