Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.
Cell lysis
Cryo-milling
Mass spectrometry
Proteomics
Single-step affinity purification
Yeast
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:
2022
2022
Historique:
entrez:
6
5
2022
pubmed:
7
5
2022
medline:
11
5
2022
Statut:
ppublish
Résumé
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to get a comprehensive picture of cellular behavior and to understand biological systems. In the past two decades, affinity purification coupled to mass spectrometry has become a powerful tool to comprehensively study interaction networks and their assemblies. To overcome initial limitations of the approach, in particular, the effect of protein and RNA degradation, loss of transient interactors, and poor overall yield of intact complexes from cell lysates, various modifications to affinity purification protocols have been devised over the years. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol as described here has been optimized for the yeast S. cerevisiae.
Identifiants
pubmed: 35524119
doi: 10.1007/978-1-0716-2257-5_12
doi:
Substances chimiques
Macromolecular Substances
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
195-223Subventions
Organisme : CIHR
ID : PJT153313
Pays : Canada
Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Gavin A, Bosche M, Krause R et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147
pubmed: 11805826
Goh K-I, Cusick ME, Valle D et al (2007) The human disease network. Proc Natl Acad Sci U S A 104:8685–8690. https://doi.org/10.1073/pnas.0701361104
pubmed: 17502601
pmcid: 1885563
Taylor IW, Linding R, Warde-Farley D et al (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27:199–204. https://doi.org/10.1038/nbt.1522
pubmed: 19182785
Ho Y, Gruhler A, Heilbut A et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183
pubmed: 11805837
Gavin A, Aloy P, Grandi P et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–636
pubmed: 16429126
Krogan N, Cagney G, Yu H et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–643
pubmed: 16554755
Costanzo MC, Hogan JD, Cusick ME et al (2000) The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28:73–76
pubmed: 10592185
pmcid: 102421
Lin D, Yin X, Wang X et al (2013) Re-annotation of protein-coding genes in the genome of Saccharomyces cerevisiae based on support vector machines. PLoS One 8(7):e64477. https://doi.org/10.1371/journal.pone.0064477
pubmed: 23874379
pmcid: 3707884
Grigoriev A (2003) On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res 31:4157–4161. https://doi.org/10.1093/nar/gkg466
pubmed: 12853633
pmcid: 165980
Collins SR, Kemmeren P, Zhao X-C et al (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6:439–450. https://doi.org/10.1074/mcp.M600381-MCP200
pubmed: 17200106
Johnson ME, Hummer G (2011) Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci U S A 108:603–608. https://doi.org/10.1073/pnas.1010954108
pubmed: 21187424
Picotti P, Bodenmiller B, Mueller LN et al (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138(4):795–806. https://doi.org/10.1016/j.cell.2009.05.051
pubmed: 19664813
pmcid: 2825542
Oeffinger M (2012) Two steps forward-one step back: advances in affinity purification mass spectrometry of macromolecular complexes. Proteomics 12(10):1591–1608. https://doi.org/10.1002/pmic.201100509
pubmed: 22592981
Cristea I, Williams R, Chait B, Rout M (2005) Fluorescent proteins as proteomic probes. Mol Cell Proteomics 4:1933–1941
pubmed: 16155292
Rigaut G, Shevchenko A, Rutz B et al (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030–1032
pubmed: 10504710
Oeffinger M, Wei KE, Rogers R et al (2007) Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 4:951–956. https://doi.org/10.1038/nmeth1101
pubmed: 17922018
Karlsson R, Jendeberg L, Nilsson B et al (1995) Direct and competitive kinetic analysis of the interaction between human IgG1 and a one domain analogue of protein a. J Immunol Methods 183:43–49
pubmed: 7602138
López-Ferrer D, Ramos-Fernández A, Martínez-Bartolomé S et al (2006) Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry. Proteomics 6(1):S4–S11. https://doi.org/10.1002/pmic.200500375
pubmed: 16534745
Capelo JL, Carreira R, Diniz M et al (2009) Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques. Anal Chim Acta 650:151–159. https://doi.org/10.1016/j.aca.2009.07.034
pubmed: 19720186
Belozerov VE, Lin Z-Y, Gingras A-C et al (2012) High-resolution protein interaction map of the Drosophila melanogaster p38 mitogen-activated protein kinases reveals limited functional redundancy. Mol Cell Biol 32:3695–3706. https://doi.org/10.1128/MCB.00232-12
pubmed: 22801366
pmcid: 3430203
Kong AT, Leprevost FV, Avtonomov DM et al (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14(5):513–520
pubmed: 28394336
pmcid: 5409104
Yu F, Teo GC, Kong AT et al (2020) Identification of modified peptides using localization-aware open search. Nat Commun 11(1):1–9
Polasky DA, Yu F, Teo GC et al (2020) Fast and comprehensive N-and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125–1132
pubmed: 33020657
pmcid: 7606558
Diament BJ, Noble WS (2011) Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res 10(9):3871–3879. https://doi.org/10.1021/pr101196n
pubmed: 21761931
pmcid: 3166376
Bjornson RD, Carriero NJ, Colangelo C et al (2008) X!!Tandem, an improved method for running X!Tandem in parallel on collections of commodity computers. J Proteome Res 7(1):293–299. https://doi.org/10.1021/pr0701198
pubmed: 17902638
Eng JK, Hoopmann MR, Jahan TA et al (2015) A deeper look into comet—implementation and features. J Am Soc Mass Spectrom 26(11):1865–1874. https://doi.org/10.1007/s13361-015-1179-x
pubmed: 26115965
pmcid: 4607604
Eng JK, Jahan TA, Hoopmann MR (2012) Comet: an open source tandem mass spectrometry sequence database search tool. Proteomics 13(1):22–24. https://doi.org/10.1002/pmic.201200439
pubmed: 23148064
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372
pubmed: 19029910
Cox J, Michalski A, Mann M (2011) Software lock mass by two-dimensional minimization of peptide mass errors. J Am Soc Mass Spectrom 22:1373–1380
pubmed: 21953191
pmcid: 3231580
Schaab C, Geiger T, Stoehr G et al (2012) Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol Cell Proteomics 11:M111.014068
pubmed: 22301388
pmcid: 3316731
Cox J, Hein MY, Luber CA et al (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13:2513–2526
pubmed: 24942700
pmcid: 4159666
Tyanova S, Temu T, Carlson A et al (2015) Visualization of LC-MS/MS proteomics data in MaxQuan. Proteomics 15:1453–1456
pubmed: 25644178
pmcid: 5024039
Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11:2301–2319
pubmed: 27809316
Liu G, Zhang JP, Larsen B et al (2010) ProHits: an integrated software platform for mass spectrometry-based interaction proteomics. Nat Biotechnol 28:1015–1017
pubmed: 20944583
pmcid: 2957308
Deutsch EW, Mendoza L, Shteynberg D et al (2010) A guided tour of the trans-proteomic pipeline. Proteomics 10(6):1150–1159. https://doi.org/10.1002/pmic.200900375
pubmed: 20101611
pmcid: 3017125
Käll L, Canterbury J, Weston J et al (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923–925
pubmed: 17952086
Käll L, Storey JD, MacCoss MJ, Noble WS (2008) Assigning confidence measures to peptides identified by tandem mass spectrometry. J Proteome Res 7(1):29–34
pubmed: 18067246
Käll L, Storey JD, Noble WS (2008) Nonparametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics 24(16):i42–i48
pubmed: 18689838
pmcid: 2732210
The M, Noble WS, MacCoss MJ, Käll L (2016) Fast and accurate protein false discovery rates on large-scale proteomics data sets with percolator 3.0. J Am Soc Mass Spectrom 27:1719–1727
pubmed: 27572102
pmcid: 5059416
Arike L, Peil L (2014) Spectral counting label-free proteomics. Methods Mol Biol 1156:213–222. https://doi.org/10.1007/978-1-4939-0685-7_14
pubmed: 24791991
Mellacheruvu D, Wright Z, Couzens AL et al (2013) The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 10:730–736. https://doi.org/10.1038/nmeth.2557
pubmed: 23921808
pmcid: 3773500
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Bondos SE, Bicknell A (2003) Detection and prevention of protein aggregation before, during, and after purification. Anal Biochem 316:223–231
pubmed: 12711344
Zhang Y, Cremer PS (2006) Interactions between macromolecules and ions: the Hofmeister series. Curr Opin Chem Biol 10:658–663. https://doi.org/10.1016/j.cbpa.2006.09.020
pubmed: 17035073
Damodaran S, Kinsella JE (1983) Dissociation of nucleoprotein complexes by chaotropic salts. FEBS Lett 158:53–57
pubmed: 6345201
Westermeier R, Naven T (2002) Proteomics in practice: a laboratory manual of proteome analysis. Wiley-VCH, Weinheim
Miseta A, Csutora P (2000) Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol Biol Evol 17:1232–1239
pubmed: 10908643
O’Connor CD, Hames BD (2008) Proteomics. Scion Publishing Limited