Abstract
In combination with bioinformatics and molecular biological techniques proteomic approaches become more and more indispensable in order to deepen our understanding of cellular functions. Since the cytoskeleton is presented by a highly dynamic network, engaged in many basic cellular functions like cell growth, migration, or intracellular transport mechanisms, many open questions remain to be clarified. Moreover, this concerns triggers of cytoskeletal remodeling or dynamics of membranous interaction partners. A proteomic description should exceed the pure listing of its constituents but rather should include functional proteomics as well as the description of protein interaction networks. Due to its mediating nature between cytosolic and membranous compartments of the cell different techniques are necessary to complete the investigation of the neuronal cytoskeleton. Within this article, we present a set of state-of-the-art approaches for further proteomic research of the cellular cytoskeleton and beyond.
Katrin Marcus and Bodo Schoenebeck contributed equally.
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Wilkins MR, Sanchez JC, Gooley AA et al (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Patterson SD, Aebersold RH (2003) Proteomics: the first decade and beyond. Nat Genet 33(Suppl):311–323
Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846
de Graauw M, Hensbergen P, van de Water B (2006) Phospho-proteomic analysis of cellular signaling. Electrophoresis 27:2676–2686
Mann M, Jensen ON (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21:255–261
Shi Y, Xu P, Qin J (2011) Ubiquitinated proteome: ready for global? Mol Cell Proteomics 10:R110.006882
Selby DS, Larsen MR, Calvano CD, Jensen ON (2008) Identification and characterization of N-glycosylated proteins using proteomics. Methods Mol Biol 484:263–276
Bodo J, Hsi ED (2011) Phosphoproteins and the dawn of functional phenotyping. Pathobiology 78:115–121
Chouchani ET, James AM, Fearnley IM et al (2011) Proteomic approaches to the characterization of protein thiol modification. Curr Opin Chem Biol 15:120–128
Thamsen M, Jakob U (2011) The redoxome: proteomic analysis of cellular redox networks. Curr Opin Chem Biol 15:113–119
Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730
Anderson NL, Anderson NG (1998) Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 19:1853–1861
Konopka G (2011) Functional genomics of the brain: uncovering networks in the CNS using a systems approach. Wiley Interdiscip Rev Syst Biol Med 3:628–648
Becker M, Schindler J, Nothwang HG (2006) Neuroproteomics—the tasks lying ahead. Electrophoresis 27:2819–2829
Bayés A, Grant SGN (2009) Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat Rev Neurosci 10:635–646
Sun C, Rosendahl AH, Ansari D, Andersson R (2011) Proteome-based biomarkers in pancreatic cancer. World J Gastroenterol 17:4845–4852
Pawa N, Wright JM, Arulampalam THA (2010) Mass spectrometry based proteomic profiling for pancreatic cancer. JOP 11:423–426
Park JP, Park MK, Yun JW (2011) Proteomic biomarkers for diagnosis in acute myocardial infarction. Biomarkers 16:1–11
Kalinina J, Peng J, Ritchie JC, Van Meir EG (2011) Proteomics of gliomas: initial biomarker discovery and evolution of technology. Neuro Oncol 13:926–942
Roti G, Stegmaier K (2012) Genetic and proteomic approaches to identify cancer drug targets. Br J Cancer 106:254–261
del Castillo C, Morales L, Alguacil LF et al (2009) Proteomic analysis of the nucleus accumbens of rats with different vulnerability to cocaine addiction. Neuropharmacology 57:41–48
Katagiri T, Hatano N, Aihara M et al (2010) Proteomic analysis of proteins expressing in regions of rat brain by a combination of SDS-PAGE with nano-liquid chromatography-quadrupole-time of flight tandem mass spectrometry. Proteome Sci 8:41
Tribl F, Marcus K, Meyer HE et al (2006) Subcellular proteomics reveals neuromelanin granules to be a lysosome-related organelle. J Neural Transm 113:741–749
Tribl F, Marcus K, Bringmann G et al (2006) Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity. J Neural Transm 113:1041–1054
Dreger M (2003) Proteome analysis at the level of subcellular structures. Eur J Biochem 270:589–599
Taylor SW, Fahy E, Ghosh SS (2003) Global organellar proteomics. Trends Biotechnol 21:82–88
Schröder BA, Wrocklage C, Hasilik A, Saftig P (2010) The proteome of lysosomes. Proteomics 10:4053–4076
Davidsson P, Folkesson S, Christiansson M et al (2002) Identification of proteins in human cerebrospinal fluid using liquid-phase isoelectric focusing as a prefractionation step followed by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation mass spectrometry. Rapid Commun Mass Spectrom 16:2083–2088
Olsen JV, Ong S-E, Mann M (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 3:608–614
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207
Biringer RG, Amato H, Harrington MG et al (2006) Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS. Brief Funct Genomic Proteomic 5:144–153
Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68:850–858
Winter D, Steen H (2011) Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. Proteomics 11:4726–4730
Lu B, McClatchy DB, Kim JY, Yates JR (2008) Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry. Proteomics 8:3947–3955
Anderson L (2005) Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J Physiol 563:23–60
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685
Weber K, Osborn M (1969) The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresis. J Biol Chem 244:4406–4412
Miller I, Crawford J, Gianazza E (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6:5385–5408
Switzer RC, Merril CR, Shifrin S (1979) A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gels. Anal Biochem 98:231–237
Westermeier R, Marouga R (2005) Protein detection methods in proteomics research. Biosci Rep 25:19–32
Chevallet M, Luche S, Rabilloud T (2006) Silver staining of proteins in polyacrylamide gels. Nat Protoc 1:1852–1858
Neuhoff V, Arold N, Taube D, Ehrhardt W (1988) Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie brilliant blue G-250 and R-250. Electrophoresis 9:255–262
Towbin H, Staehelin T, Gordon J (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A 76:4350–4354
Jensen EC (2012) The basics of Western blotting. Anat Rec (Hoboken) 295:369–371
Müller T, Loosse C, Schrötter A et al (2011) The AICD interacting protein DAB1 is up-regulated in Alzheimer frontal cortex brain samples and causes deregulation of proteins involved in gene expression changes. Curr Alzheimer Res 8:573–582
Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26:231–243
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021
Taylor NL, Heazlewood JL, Millar AH (2011) The Arabidopsis thaliana 2-D gel mitochondrial proteome: refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications. Proteomics 11:1720–1733
Klose J, Kobalz U (1995) Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16:1034–1059
Bjellqvist B, Ek K, Righetti PG et al (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6:317–339
Görg A, Postel W, Günther S (1988) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9:531–546
Görg A, Drews O, Lück C et al (2009) 2-DE with IPGs. Electrophoresis 30(Suppl 1):S122–S132
Luhn S, Berth M, Hecker M, Bernhardt J (2003) Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics 3:1117–1127
Dowsey AW, English JA, Lisacek F et al (2010) Image analysis tools and emerging algorithms for expression proteomics. Proteomics 10:4226–4257
Schägger H, von Jagow G (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199:223–231
Zahedi R-P, Meisinger C, Sickmann A (2005) Two-dimensional benzyldimethyl-n-hexadecylammonium chloride/SDS-PAGE for membrane proteomics. Proteomics 5:3581–3588
Hartinger J, Stenius K, Högemann D, Jahn R (1996) 16-BAC/SDS-PAGE: a two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal Biochem 240:126–133
Macfarlane DE (1989) Two dimensional benzyldimethyl-n-hexadecylammonium chloride-sodium dodecyl sulfate preparative polyacrylamide gel electrophoresis: a high capacity high resolution technique for the purification of proteins from complex mixtures. Anal Biochem 176:457–463
Helling S, Schmitt E, Joppich C et al (2006) 2-D differential membrane proteome analysis of scarce protein samples. Proteomics 6:4506–4513
Eley MH, Burns PC, Kannapell CC, Campbell PS (1979) Cetyltrimethylammonium bromide polyacrylamide gel electrophoresis: estimation of protein subunit molecular weights using cationic detergents. Anal Biochem 92:411–419
Rais I, Karas M, Schägger H (2004) Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics 4:2567–2571
Unlü M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077
Alban A, David SO, Bjorkesten L et al (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3:36–44
Mitulovic G, Mechtler K (2006) HPLC techniques for proteomics analysis-a short overview of latest developments. Brief Funct Genomic Proteomic 5:249–260
Carr PW, Stoll DR, Wang X (2011) Perspectives on recent advances in the speed of high-performance liquid chromatography. Anal Chem 83:1890–1900
Tao D, Zhang L, Shan Y, Liang Z, Zhang Y (2011) Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research. Anal Bioanal Chem 399:229–241
Küster B, Wheeler SF, Hunter AP et al (1997) Sequencing of N-linked oligosaccharides directly from protein gels: in-gel deglycosylation followed by matrix-assisted laser desorption/ionization mass spectrometry and normal-phase high-performance liquid chromatography. Anal Biochem 250:82–101
Marcus K, Joppich C, May C et al (2009) High-resolution 2DE. Methods Mol Biol 519:221–240
Neville B (1998) Reversed-phase HPLC. In: Rapley R, Walker JM (eds) Molecular biomethods handbook, 1st edn. Humana, New York
Erni F, Steuer W, Bosshardt H (1987) Automation and validation of HPLC-systems. Chromatographia 24:201–207
Köcher T, Swart R, Mechtler K (2011) Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal Chem 83:2699–2704
Whitehouse CM, Dreyer RN, Yamashita M, Fenn JB (1985) Electrospray interface for liquid chromatographs and mass spectrometers. Anal Chem 57:675–679
Washburn MP, Wolters D, Yates JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242–247
Zhang X, Fang A, Riley CP et al (2010) Multi-dimensional liquid chromatography in proteomics–a review. Anal Chim Acta 664:101–113
Wang Z, Hill S, Luther JM et al (2012) Proteomic analysis of urine exosomes by multidimensional protein identification technology (MudPIT). Proteomics 12:329–338
Chervet JP, Ursem M, Salzmann JP (1996) Instrumental requirements for nanoscale liquid chromatography. Anal Chem 68:1507–1512
Contrepois K, Ezan E, Mann C, Fenaille F (2010) Ultra-high performance liquid chromatography-mass spectrometry for the fast profiling of histone post-translational modifications. J Proteome Res 9:5501–5509
Guillarme D, Ruta J, Rudaz S, Veuthey J-L (2010) New trends in fast and high-resolution liquid chromatography: a critical comparison of existing approaches. Anal Bioanal Chem 397:1069–1082
Jorgenson JW (2010) Capillary liquid chromatography at ultrahigh pressures. Annu Rev Anal Chem (Palo Alto Calif) 3:129–150
Glish GL, Vachet RW (2003) The basics of mass spectrometry in the twenty-first century. Nat Rev Drug Discov 2:140–150
Xie F, Liu T, Qian W-J et al (2011) Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 286:25443–25449
Han J, Datla R, Chan S, Borchers CH (2009) Mass spectrometry-based technologies for high-throughput metabolomics. Bioanalysis 1:1665–1684
Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60:2299–2301
Nyman TA (2001) The role of mass spectrometry in proteome studies. Biomol Eng 18:221–227
Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71
Zaluzec EJ, Gage DA, Watson JT (1995) Matrix-assisted laser desorption ionization mass spectrometry: applications in peptide and protein characterization. Protein Expr Purif 6:109–123
Karas M, Glückmann M, Schäfer J (2000) Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors. J Mass Spectrom 35:1–12
Nordhoff E, Egelhofer V, Giavalisco P et al (2001) Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures. Electrophoresis 22:2844–2855
Stühler K, Meyer HE (2004) MALDI: more than peptide mass fingerprints. Curr Opin Mol Ther 6:239–248
Loo JA, Udseth HR, Smith RD (1989) Peptide and protein analysis by electrospray ionization-mass spectrometry and capillary electrophoresis-mass spectrometry. Anal Chem 179:404–412
Cech NB, Enke CG (2001) Practical implications of some recent studies in electrospray ionization fundamentals. Mass Spectrom Rev 20:362–387
Iribarne JV (1976) On the evaporation of small ions from charged droplets. J Chem Phys 64:2287
Dole M (1968) Molecular beams of macroions. J Chem Phys 49:2240
Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312:212–217
Wollnik H (1993) Time-of-flight mass analyzers. Mass Spectrom Rev 12:89–114
Balogh MP (2004) Debating resolution and mass accuracy in mass spectrometry. Spectroscopy 19:34–40
Schwartz JC, Senko MW, Syka JEP (2002) A two-dimensional quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom 13:659–669
March RE (2000) Quadrupole ion trap mass spectrometry: a view at the turn of the century. Int J Mass Spectrom 200:285–312
Wilm M, Neubauer G, Mann M (1996) Parent ion scans of unseparated peptide mixtures. Anal Chem 68:527–533
Steen H, Küster B, Fernandez M et al (2001) Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal Chem 73:1440–1448
Hunter AP, Games DE (1994) Chromatographic and mass spectrometric methods for the identification of phosphorylation sites in phosphoproteins. Rapid Commun Mass Spectrom 8:559–570
Schlosser A, Pipkorn R, Bossemeyer D, Lehmann WD (2001) Analysis of protein phosphorylation by a combination of elastase digestion and neutral loss tandem mass spectrometry. Anal Chem 73:170–176
Yocum AK, Chinnaiyan AM (2009) Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic 8:145–157
Busch F, Paul W (1961) Isotopentrennung mit dem elektrischen Massenfilter. Zeitschrift für Physik 164:581–587
Douglas DJ, Frank AJ, Mao D (2005) Linear ion traps in mass spectrometry. Mass Spectrom Rev 24:1–29
Mikesh LM, Ueberheide B, Chi A et al (2006) The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta 1764:1811–1822
Chi A, Huttenhower C, Geer LY et al (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A 104:2193–2198
Perdivara I, Petrovich R, Allinquant B et al (2009) Elucidation of O-glycosylation structures of the beta-amyloid precursor protein by liquid chromatography-mass spectrometry using electron transfer dissociation and collision induced dissociation. J Proteome Res 8:631–642
Alley WR, Mechref Y, Novotny MV (2009) Characterization of glycopeptides by combining collision-induced dissociation and electron-transfer dissociation mass spectrometry data. Rapid Commun Mass Spectrom 23:161–170
Wiesner J, Premsler T, Sickmann A (2008) Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8:4466–4483
Wang Y, Franzen J (1992) The non-linear resonance QUISTOR Part 1. Potential distribution in hyperboloidal QUISTORs. Int J Mass Spectrom Ion Process 112:167–178
Wang Y, Franzen J, Wanczek KP (1993) The non-linear resonance ion trap. Part 2. A general theoretical analysis. Int J Mass Spectrom Ion Process 124:125–144
Wang Y, Franzen J (1994) The non-linear ion trap. Part 3. Multipole components in three types of practical ion trap. Int J Mass Spectrom Ion Process 132:155–172
Franzen J (1993) The non-linear ion trap. Part 4. Mass selective instability scan with multipole superposition. Int J Mass Spectrom Ion Process 125:165–170
Franzen J (1994) The non-linear ion trap. Part 5. Nature of non-linear resonances and resonant ion ejection. Int J Mass Spectrom Ion Process 130:15–40
Marshall AG, Hendrickson CL, Jackson GS (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17:1–35
Comisarow MB, Marshall AG (1974) Fourier transform ion cyclotron resonance spectroscopy. Chem Phys Lett 25:282–283
Goodlett DR, Bruce JE, Anderson GA et al (2000) Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal Chem 72:1112–1118
Hu Q, Noll RJ, Li H et al (2005) The orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443
Perry RH, Cooks RG, Noll RJ (2008) Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom Rev 27:661–699
Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72:1156–1162
Scigelova M, Makarov A (2006) Orbitrap mass analyzer–overview and applications in proteomics. Proteomics 6(Suppl 2):16–21
Aebersold R, Goodlett DR (2001) Mass spectrometry in proteomics. Chem Rev 101:269–295
Spengler B, Kirsch D, Kaufmann R, Jaeger E (1992) Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun Mass Spectrom 6:105–108
de Hoffmann E (1996) Tandem mass spectrometry: a primer. J Mass Spectrom 31:129–137
Steen H, Küster B, Mann M (2001) Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning. J Mass Spectrom 36:782–790
Aldini G, Regazzoni L, Orioli M et al (2008) A tandem MS precursor-ion scan approach to identify variable covalent modification of albumin Cys34: a new tool for studying vascular carbonylation. J Mass Spectrom 43:1470–1481
Hopfgartner G, Varesio E, Tschäppät V et al (2004) Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J Mass Spectrom 39:845–855
Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 214:397–408
Boyd RK (1994) Linked-scan techniques for MS/MS using tandem-in-space instruments. Mass Spectrom Rev 13:359–410
Carr SA, Huddleston MJ, Annan RS (1996) Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal Biochem 239:180–192
Huddleston MJ, Bean MF, Carr SA (1993) Collisional fragmentation of glycopeptides by electrospray ionization LC/MS and LC/MS/MS: methods for selective detection of glycopeptides in protein digests. Anal Biochem 65:877–884
Gadgil HS, Bondarenko PV, Treuheit MJ, Ren D (2007) Screening and sequencing of glycated proteins by neutral loss scan LC/MS/MS method. Anal Biochem 79:5991–5999
Langenfeld E, Zanger UM, Jung K et al (2009) Mass spectrometry-based absolute quantification of microsomal cytochrome P450 2D6 in human liver. Proteomics 9:2313–2323
Unwin RD, Griffiths JR, Leverentz MK et al (2005) Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol Cell Proteomics 4:1134–1144
Annan RS, Carr SA (1997) The essential role of mass spectrometry in characterizing protein structure: mapping posttranslational modifications. J Protein Chem 16:391–402
Williamson BL, Marchese J, Morrice NA (2006) Automated identification and quantification of protein phosphorylation sites by LC/MS on a hybrid triple quadrupole linear ion trap mass spectrometer. Mol Cell Proteomics 5:337–346
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567
Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989
Biemann K (1990) Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol 193:886–887
Zhang W, Chait BT (2000) ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 72:2482–2489
McLafferty FW, Tureek F (eds) (1993) Interpretation of mass spectra, 4th edn. University Science, California
Zhu W, Smith JW, Huang C-M (2010) Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2010:840518
Ong S-E, Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1:252–262
Bantscheff M, Schirle M, Sweetman G et al (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389:1017–1031
Bettmer J (2010) Application of isotope dilution ICP-MS techniques to quantitative proteomics. Anal Bioanal Chem 397:3495–3502
Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999
Ross PL, Huang YN, Marchese JN et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169
Schmidt A, Kellermann J, Lottspeich F (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5:4–15
Yao X, Freas A, Ramirez J et al (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73:2836–2842
Staes A, Demol H, Van Damme J et al (2004) Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res 3:786–791
Shiio Y, Aebersold R (2006) Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc 1:139–145
Thompson A, Schäfer J, Kuhn K et al (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75:1895–1904
Boehm AM, Pütz S, Altenhöfer D (2007) Precise protein quantification based on peptide quantification using iTRAQ. BMC Bioinformatics 8:214
Aggarwal K, Choe LH, Lee KH (2006) Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct Genomics Proteomics 5:112–120
Bantscheff M, Boesche M, Eberhard D et al (2008) Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol Cell Proteomics 7:1702–1713
Dayon L, Turck N, Scherl A et al (2010) From relative to absolute quantification of tryptic peptides with tandem mass tags: application to cerebrospinal fluid. Chimia (Aarau) 64:132–135
Brunner A, Keidel E-M, Dosch D et al (2010) ICPLQuant—a software for non-isobaric isotopic labeling proteomics. Proteomics 10:315–326
Ong S-E, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386
Amanchy R, Kalume DE, Iwahori A et al (2005) Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res 4:1661–1671
Meierhofer D, Wang X, Huang L, Kaiser P (2008) Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res 7:4566–4576
Oeljeklaus S, Reinartz BS, Wolf J et al (2012) Identification of core components and transient interactors of the peroxisomal importomer by dual-track stable isotope labeling with amino acids in cell culture analysis. J Proteome Res 11:2567–2580
Krijgsveld J, Ketting RF, Mahmoudi T et al (2003) Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 21:927–931
Larance M, Bailly AP, Pourkarimi E et al (2011) Stable-isotope labeling with amino acids in nematodes. Nat Methods 8:849–851
Sury MD, Chen J-X, Selbach M (2010) The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics 9:2173–2183
Krüger M, Moser M, Ussar S et al (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134:353–364
Walther DM, Mann M (2011) Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging. Mol Cell Proteomics 10:M110.004523
Oda Y, Huang K, Cross FR et al (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 96:6591–6596
Old WM, Meyer-Arendt K, Aveline-Wolf L et al (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4:1487–1502
Neilson KA, Ali N, Muralidharan S et al (2011) Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 11:535–553
Carvalho PC, Hewel J, Barbosa VC, Yates JR (2008) Identifying differences in protein expression levels by spectral counting and feature selection. Genet Mol Res 7:342–356
Liu H, Sadygov RG, Yates JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201
Bondarenko PV, Chelius D, Shaler TA (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74:4741–4749
Chelius D, Bondarenko PV (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1:317–323
Higgs RE, Knierman MD, Gelfanova V et al (2005) Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res 4:1442–1450
Wang G, Wu WW, Zeng W et al (2006) Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes. J Proteome Res 5:1214–1223
Zybailov B, Coleman MK, Florens L, Washburn MP (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77:6218–6224
Pan S, Aebersold R, Chen R et al (2009) Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 8:787–797
Brun V, Masselon C, Garin J, Dupuis A (2009) Isotope dilution strategies for absolute quantitative proteomics. J Proteomics 72:740–749
Gerber SA, Rush J, Stemman O et al (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100:6940–6945
Stahl-Zeng J, Lange V, Ossola R et al (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 6:1809–1817
Anderson L, Hunter CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5:573–588
Keshishian H, Addona T, Burgess M et al (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 6:2212–2229
Brun V, Dupuis A, Adrait A et al (2007) Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 6:2139–2149
Brownridge P, Holman SW, Gaskell SJ et al (2011) Global absolute quantification of a proteome: challenges in the deployment of a QconCAT strategy. Proteomics 11:2957–2970
Pratt JM, Simpson DM, Doherty MK et al (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc 1:1029–1043
Dupuis A, Hennekinne J-A, Garin J, Brun V (2008) Protein standard absolute quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics 8:4633–4636
Kandel ER, Schwartz JH, Jessell TM (eds) (2000) Principles of neural science, 4th edn. McGraw-Hill, New York
McEwen BS (2012) The ever-changing brain: cellular and molecular mechanisms for the effects of stressful experiences. Dev Neurobiol 72:878–890
Gogolla N, Galimberti I, Caroni P (2007) Structural plasticity of axon terminals in the adult. Curr Opin Neurobiol 17:516–524
Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727–730
Rabilloud T (2003) Membrane proteins ride shotgun. Nat Biotechnol 21:508–510
Macher BA, Yen T-Y (2007) Proteins at membrane surfaces-a review of approaches. Mol Biosyst 3:705–713
Santoni V, Molloy M, Rabilloud T (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21:1054–1070
Josic D, Zeilinger K (1996) Membrane proteins. Methods Enzymol 271:113–134
Roy I, Mondal K, Gupta MN (2007) Leveraging protein purification strategies in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 849:32–42
Clifton JG, Li X, Reutter W et al (2007) Comparative proteomics of rat liver and Morris hepatoma 7777 plasma membranes. J Chromatogr B Analyt Technol Biomed Life Sci 849:293–301
Clifton JG, Brown MK, Huang F et al (2006) Identification of members of the annexin family in the detergent-insoluble fraction of rat Morris hepatoma plasma membranes. J Chromatogr A 1123:205–211
Rabilloud T (2009) Membrane proteins and proteomics: love is possible, but so difficult. Electrophoresis 30(Suppl 1):S174–S180
Josic D, Clifton JG (2007) Mammalian plasma membrane proteomics. Proteomics 7:3010–3029
Cordwell SJ, Thingholm TE (2010) Technologies for plasma membrane proteomics. Proteomics 10:611–627
Tauber R, Reutter W (1978) Protein degradation in the plasma membrane of regenerating liver and Morris hepatomas. Eur J Biochem 83:37–45
Cao R, Li X, Liu Z et al (2006) Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J Proteome Res 5:634–642
Schindler J, Lewandrowski U, Sickmann A et al (2006) Proteomic analysis of brain plasma membranes isolated by affinity two-phase partitioning. Mol Cell Proteomics 5:390–400
Blonder J, Terunuma A, Conrads TP et al (2004) A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol 123:691–699
Navarre C, Degand H, Bennett KL et al (2002) Subproteomics: identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae. Proteomics 2:1706–1714
Zhang L, Xie J, Wang X et al (2005) Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins. Proteomics 5:4510–4524
Chang PS, Absood A, Linderman JJ, Omann GM (2004) Magnetic bead isolation of neutrophil plasma membranes and quantification of membrane-associated guanine nucleotide binding proteins. Anal Biochem 325:175–184
Zhang W, Zhou G, Zhao Y et al (2003) Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis 24:2855–2863
Elia G (2008) Biotinylation reagents for the study of cell surface proteins. Proteomics 8:4012–4024
Zhao Y, Zhang W, Kho Y, Zhao Y (2004) Proteomic analysis of integral plasma membrane proteins. Anal Chem 76:1817–1823
Zhang W, Wang H, Wang J et al (2006) Multiresidue determination of zeranol and related compounds in bovine muscle by gas chromatography/mass spectrometry with immunoaffinity cleanup. J AOAC Int 89:1677–1681
Lawson EL, Clifton JG, Huang F et al (2006) Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes. Electrophoresis 27:2747–2758
Ghosh D, Krokhin O, Antonovici M et al (2004) Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. J Proteome Res 3:841–850
Kullolli M, Hancock WS, Hincapie M (2008) Preparation of a high-performance multi-lectin affinity chromatography (HP-M-LAC) adsorbent for the analysis of human plasma glycoproteins. J Sep Sci 31:2733–2739
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The authors gratefully note Helga Schulze for image editing.
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Loosse, C., Marcus, K., Schoenebeck, B. (2013). Principles of Proteomic Approaches to the Cytoskeleton. In: Dermietzel, R. (eds) The Cytoskeleton. Neuromethods, vol 79. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-266-7_5
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