Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.
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References
J. B. Fenn M. Mann C. K. Meng S. F. Wong C. M. Whitehouse (1989) ArticleTitleElectrospray ionization for mass spectrometry of large biomolecules Science 246 64–71 Occurrence Handle2675315
M. Karas F. Hillenkamp (1988) ArticleTitleLaser desorption ionization of proteins with molecular masses exceeding 10,000 daltons Anal. Chem. 60 2299–2301 Occurrence Handle10.1021/ac00171a028 Occurrence Handle3239801
J. R. Yates SuffixIII (2004) ArticleTitleMass spectral analysis in proteomics Annu. Rev. Biophys. Biomol. Struct. 33 297–316 Occurrence Handle10.1146/annurev.biophys.33.111502.082538 Occurrence Handle15139815
R. Aebersold M. Mann (2003) ArticleTitleMass spectrometry-based proteomics Nature 422 198–207 Occurrence Handle10.1038/nature01511 Occurrence Handle12634793
R. Aebersold D. R. Goodlett (2001) ArticleTitleMass spectrometry in proteomics Chem. Rev. 101 269–295
K. R. Jonscher J. R. Yates SuffixIII (1997) ArticleTitleThe quadrupole ion trap mass spectrometer—a small solution to a big challenge Anal. Biochem. 244 1–15 Occurrence Handle10.1006/abio.1996.9877 Occurrence Handle9025900
J. W. Hager (2002) ArticleTitleA new linear ion trap mass spectrometer Rapid Commun. Mass Spectrom. 16 512–526 Occurrence Handle10.1002/rcm.607
J. C. Schwartz M. W. Senko J. E. Syka (2002) ArticleTitleA two-dimensional quadrupole ion trap mass spectrometer J. Am. Soc. Mass Spectrom. 13 659–669 Occurrence Handle10.1016/S1044-0305(02)00384-7 Occurrence Handle12056566
W. V. Bienvenut C. Deon C. Pasquarello J. M. Campbell J. C. Sanchez M. L. Vestal D. F. Hochstrasser (2002) ArticleTitleMatrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins Proteomics 2 868–876 Occurrence Handle10.1002/1615-9861(200207)2:7<868::AID-PROT868>3.0.CO;2-D Occurrence Handle12124932
K. F. Medzihradszky J. M. Campbell M. A. Baldwin A. M. Falick P. Juhasz M. L. Vestal A. L. Burlingame (2000) ArticleTitleThe characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer Anal. Chem. 72 552–558 Occurrence Handle10.1021/ac990809y Occurrence Handle10695141
I. V. Chernushevich A. V. Loboda B. A. Thomson (2001) ArticleTitleAn introduction to quadrupole-time-of-flight mass spectrometry J. Mass Spectrom. 36 849–865 Occurrence Handle10.1002/jms.207 Occurrence Handle11523084
A. V. Loboda A. N. Krutchinsky M. Bromirski W. Ens K. G. Standing (2000) ArticleTitleA tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance Rapid Commun. Mass Spectrom. 14 1047–1057 Occurrence Handle10.1002/1097-0231(20000630)14:12<1047::AID-RCM990>3.0.CO;2-E Occurrence Handle10861986
N. Tang P. Tornatore S. R. Weinberger (2004) ArticleTitleCurrent developments in SELDI affinity technology Mass Spectrom. Rev. 23 34–44 Occurrence Handle10.1002/mas.10066 Occurrence Handle14625891
G. L. Wright SuffixJr. (2002) ArticleTitleSELDI proteinchip MS: a platform for biomarker discovery and cancer diagnosis Expert Rev. Mol. Diagn. 2 549–563 Occurrence Handle10.1586/14737159.2.6.549 Occurrence Handle12465452
Y. F. Zhang D. L. Wu M. Guan W. W. Liu Z. Wu Y. M. Chen W. Z. Zhang Y. Lu (2004) ArticleTitleTree analysis of mass spectral urine profiles discriminates transitional cell carcinoma of the bladder from noncancer patient Clin. Biochem. 37 772–779 Occurrence Handle10.1016/j.clinbiochem.2004.04.002 Occurrence Handle15329315
K. A. Baggerly J. S. Morris K. R. Coombes (2004) ArticleTitleReproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments Bioinformatics 20 777–785 Occurrence Handle10.1093/bioinformatics/btg484 Occurrence Handle14751995
J. Wei J. M. Buriak G. Siuzdak (1999) ArticleTitleDesorption-ionization mass spectrometry on porous silicon Nature 399 243–246 Occurrence Handle10.1038/20400 Occurrence Handle10353246
Z. Shen E. P. Go A. Gamez J. V. Apon V. Fokin M. Greig M. Ventura J. E. Crowell O. Blixt J. C. Paulson R. C. Stevens M. G. Finn G. Siuzdak (2004) ArticleTitleA mass spectrometry plate reader: monitoring enzyme activity and inhibition with a Desorption/Ionization on Silicon (DIOS) platform Chembiochem. 5 921–927 Occurrence Handle10.1002/cbic.200400008 Occurrence Handle15239048
S. A. Trauger E. P. Go Z. Shen J. V. Apon B. J. Compton E. S. Bouvier M. G. Finn G. Siuzdak (2004) ArticleTitleHigh sensitivity and analyte capture with desorption/ionization mass spectrometry on silylated porous silicon Anal. Chem. 76 4484–4489 Occurrence Handle10.1021/ac049657j Occurrence Handle15283591
Bogdanov, B. and Smith, R. D. (2004) Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom. Rev. DOI 10.1002/mas.20015.
R. M. Heeren A. J. Kleinnijenhuis L. A. McDonnell T. H. Mize (2004) ArticleTitleA mini-review of mass spectrometry using high-performance FTICR-MS methods Anal. Bioanal. Chem. 378 1048–1058 Occurrence Handle10.1007/s00216-003-2446-4 Occurrence Handle14716471
S. K. Sze Y. Ge H. Oh F. W. McLafferty (2002) ArticleTitleTop-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue Proc. Natl. Acad. Sci. USA 99 1774–1779 Occurrence Handle10.1073/pnas.251691898 Occurrence Handle11842225
W. Schrader H. W. Klein (2004) ArticleTitleLiquid chromatography/fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS): an early overview Anal. Bioanal. Chem. 379 1013–1024 Occurrence Handle10.1007/s00216-004-2675-1 Occurrence Handle15221183
J. E. Syka J. A. Marto D. L. Bai S. Horning M. W. Senko J. C. Schwartz B. Ueberheide B. Garcia S. Busby T. Muratore J. Shabanowitz D. F. Hunt (2004) ArticleTitleNovel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications J. Proteome. Res. 3 621–626 Occurrence Handle10.1021/pr0499794 Occurrence Handle15253445
B. E. Wilcox C. L. Hendrickson A. G. Marshall (2002) ArticleTitleImproved ion extraction from a linear octopole ion trap: SIMION analysis and experimental demonstration J. Am. Soc. Mass Spectrom. 13 1304–1312 Occurrence Handle10.1016/S1044-0305(02)00622-0 Occurrence Handle12443021
J. V. Olsen M. Mann (2004) ArticleTitleImproved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation Proc. Natl. Acad. Sci. U.S.A. 101 13,417–13422
A. Brock D. M. Horn E. C. Peters C. M. Shaw C. Ericson Q. T. Phung A. R. Salomon (2003) ArticleTitleAn automated matrix-assisted laser desorption/ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer for “Bottom-Up” proteomics Anal. Chem. 75 3419–3428 Occurrence Handle10.1021/ac034215d Occurrence Handle14570192
D. J. Douglas A. J. Frank D. Mao (2005) ArticleTitleLinear ion traps in mass spectrometry Mass Spectrom. Rev. 24 1–29 Occurrence Handle10.1002/mas.20004 Occurrence Handle15389865
G. Hopfgartner E. Varesio V. Tschappat C. Grivet E. Bourgogne L. A. Leuthold (2004) ArticleTitleTriple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules J. Mass Spectrom. 39 845–855 Occurrence Handle10.1002/jms.659 Occurrence Handle15329837
S. M. Patrie J. P. Charlebois D. Whipple N. L. Kelleher C. L. Hendrickson J. P. Quinn A. G. Marshall B. Mukhopadhyay (2004) ArticleTitleConstruction of a hybrid quadrupole/Fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa J. Am. Soc. Mass Spectrom. 15 1099–1108 Occurrence Handle10.1016/j.jasms.2004.04.031 Occurrence Handle15234368
Y. Shen N. Tolic C. Masselon L. Pasa-Tolic D. G. Camp SuffixII K. K. Hixson R. Zhao G. A. Anderson R. D. Smith (2004) ArticleTitleUltrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS Anal. Chem. 76 144–154 Occurrence Handle10.1021/ac030096q Occurrence Handle14697044
J. S. Cottrell (1994) ArticleTitleProtein identification by peptide mass fingerprinting Pept. Res. 7 115–124 Occurrence Handle8081066
J. K. Eng A. L. McCormack J. R. R. Yates (1994) ArticleTitleAn 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 Occurrence Handle10.1016/1044-0305(94)80016-2
M. Mann M. Wilm (1994) ArticleTitleError-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 66 4390–4399 Occurrence Handle10.1021/ac00096a002 Occurrence Handle7847635
D. N. Perkins D. J. Pappin D. M. Creasy J. S. Cottrell (1999) ArticleTitleProbability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 3551–3567 Occurrence Handle10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 Occurrence Handle10612281
Kleiner, O. and Godovac-Zimmermann, J. (2005) Proteomics of signal transduction pathways. In: Signalling Pathways in Liver Diseases. Springer Verlag, Heidelberg, Germany, pp. 417–431.
C. Stannard L. R. Brown J. Godovac-Zimmermann (2004) ArticleTitleNew paradigms in cellular function and the need for top-down proteomics analyses Curr. Proteom. 1 13–25
Wang, H. and Hanash, S. (2004) Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom. Rev. DOI 10.1002/mas.20018.
A. J. Link (2002) ArticleTitleMultidimensional peptide separations in proteomics Trends Biotechnol. 20 S8–13 Occurrence Handle10.1016/S1471-1931(02)00202-1 Occurrence Handle12570153
Godovac-Zimmermann, J., Kleiner, O., and Drukier, A. K. (2005) Perspectives in spicing up proteomics with splicing, Proteomics 5:699–709.
G. E. Reid S. A. McLuckey (2002) ArticleTitle‘Top down’ protein characterization via tandem mass spectrometry J. Mass Spectrom. 37 663–675 Occurrence Handle10.1002/jms.346 Occurrence Handle12124999
F. Kjeldsen K. F. Haselmann B. A. Budnik E. S. Sorensen R. A. Zubarev (2003) ArticleTitleComplete characterization of posttranslational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage Anal. Chem. 75 2355–2361 Occurrence Handle10.1021/ac026295b Occurrence Handle12918977
A. J. Link J. Eng D. M. Schieltz E. Carmack G. J. Mize D. R. Morris B. M. Garvik J. R. Yates (1999) ArticleTitleDirect analysis of protein complexes using mass spectrometry Nat. Biotechnol. 17 676–682 Occurrence Handle10.1038/10890 Occurrence Handle10404161
D. A. Wolters M. P. Washburn J. R. Yates SuffixIII (2001) ArticleTitleAn automated multidimensional protein identification technology for shotgun proteomics Anal. Chem. 73 5683–5690 Occurrence Handle10.1021/ac010617e Occurrence Handle11774908
D. Lin A. J. Alpert J. R. Yates SuffixIII (2001) ArticleTitleMultidimensional protein identification technology as an effective tool for proteomics Am. Genom. Proteomic Technol. 1 38–46
M. P. Washburn D. Wolters J. R. Yates SuffixIII (2001) ArticleTitleLarge-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 19 242–247 Occurrence Handle10.1038/85686 Occurrence Handle11231557
M. S. Lipton L. Pasa-Tolic G. A. Anderson D. J. Anderson D. L. Auberry J. R. Battista M. J. Daly J. Fredrickson K. K. Hixson H. Kostandarithes C. Masselon L. M. Markillie R. J. Moore M. F. Romine Y. Shen E. Stritmatter N. Tolic H. R. Udseth A. Venkateswaran K. K. Wong R. Zhao R. D. Smith (2002) ArticleTitleGlobal analysis of the Deinococcus radiodurans proteome by using accurate mass tags Proc. Natl. Acad. Sci. USA 99 11,049–11054
R. D. Smith G. A. Anderson M. S. Lipton C. Masselon L. Paa-Tolic´ Y. Shen H. R. Udseth (2002) ArticleTitleThe use of accurate mass tags for high-throughput microbial proteomics OMICS 6 61–90 Occurrence Handle10.1089/15362310252780843 Occurrence Handle11881835
F. Meng B. J. Cargile L. M. Miller A. J. Forbes J. R. Johnson N. L. Kelleher (2001) ArticleTitleInformatics and multiplexing of intact protein identification in bacteria and the archaea Nat. Biotechnol. 19 952–957 Occurrence Handle10.1038/nbt1001-952 Occurrence Handle11581661
Shakib, K., Norman, J. T., Fine, L. G., Brown, L. R., and Godovac-Zimmermann, J. (2005) Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis and cancer may meet in the nucleus, Proteomics. 5:2819–2838.
J. Lill (2003) ArticleTitleProteomic tools for quantitation by mass spectrometry Mass Spectrom. Rev. 22 182–194 Occurrence Handle10.1002/mas.10048 Occurrence Handle12838544
D. E. Mason D. C. Liebler (2003) ArticleTitleQuantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate J. Proteome Res. 2 265–272 Occurrence Handle10.1021/pr0255856 Occurrence Handle12814266
Y. Oda K. Huang F. R. Cross D. Cowburn B. T. Chait (1999) ArticleTitleAccurate quantitation of protein expression and site-specific phosphorylation Proc. Natl. Acad. Sci. U.S.A. 96 6591–6596 Occurrence Handle10.1073/pnas.96.12.6591 Occurrence Handle10359756
J. Pasa-Tolic P. K. Jensen G. A. Anderson M. S. Lipton K. K. Peden S. Martinovic N. Tolic J. E. Bruce R. D. Smith (1999) ArticleTitleHigh throughput proteome-wide precision measurements of protein expression using mass spectrometry J. Am. Chem. Soc. 121 7949–7950 Occurrence Handle10.1021/ja991063o
M. P. Washburn R. Ulaszek C. Deciu D. M. Schieltz J. R. Yates SuffixIII (2002) ArticleTitleAnalysis of quantitative proteomic data generated via multidimensional protein identification technology Anal. Chem. 74 1650–1657 Occurrence Handle10.1021/ac015704l Occurrence Handle12043600
A. P. Leenheer ParticleDe L. M. Thienport (1992) ArticleTitleApplication of isotope dilution-mass spectrometry in clinical chemistry, pharmacokinetics, and toxicology Mass Spectrom. Rev. 11 249–307 Occurrence Handle10.1002/mas.1280110402
S. E. Ong B. Blagoev I. Kratchmarova D. B. Kristensen H. Steen A. Pandey M. Mann (2002) ArticleTitleStable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell Proteomics. 1 376–386 Occurrence Handle10.1074/mcp.M200025-MCP200 Occurrence Handle12118079
S. E. Ong I. Kratchmarova M. Mann (2003) ArticleTitleProperties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC) J. Proteome Res. 2 173–181 Occurrence Handle10.1021/pr0255708 Occurrence Handle12716131
N. Ibarrola H. Molina A. Iwahori A. Pandey (2004) ArticleTitleA novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine J. Biol. Chem. 279 15805–15813 Occurrence Handle10.1074/jbc.M311714200 Occurrence Handle14739304
B. Blagoev S. E. Ong I. Kratchmarova M. Mann (2004) ArticleTitleTemporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics Nat. Biotechnol. 22 1139–1145 Occurrence Handle10.1038/nbt1005 Occurrence Handle15314609
J. Krijgsveld R. F. Ketting T. Mahmoudi J. Johansen M. Artal-Sanz C. P. Verrijzer R. H. Plasterk A. J. Heck (2003) ArticleTitleMetabolic labeling of C. elegans and D. melanogaster for quantitative proteomics Nat. Biotechnol. 21 927–931 Occurrence Handle10.1038/nbt848 Occurrence Handle12858183
S. P. Gygi B. Rist S. A. Gerber F. Turecek M. H. Gelb R. Aebersold (1999) ArticleTitleQuantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 17 994–999 Occurrence Handle10.1038/13690 Occurrence Handle10504701
M. B. Goshe T. D. Veenstra E. A. Panisko T. P. Conrads N. H. Angell R. D. Smith (2002) ArticleTitlePhosphoprotein isotope-coded affinity tags: application to the enrichment and identification of low-abundance phosphoproteins Anal. Chem. 74 607–616 Occurrence Handle10.1021/ac015528g Occurrence Handle11838682
Y. Qiu E. A. Sousa R. M. Hewick J. H. Wang (2002) ArticleTitleAcid-labile isotope-coded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures Anal. Chem. 74 4969–4979 Occurrence Handle10.1021/ac0256437 Occurrence Handle12380819
H. Zhou J. A. Ranish J. D. Watts R. Aebersold (2002) ArticleTitleQuantitative proteome analysis by solid-phase isotope tagging and mass spectrometry Nat. Biotechnol. 20 512–515 Occurrence Handle10.1038/nbt0502-512 Occurrence Handle11981568
S. P. Gygi B. Rist T. J. Griffin J. Eng R. Aebersold (2002) ArticleTitleProteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags J. Proteome Res. 1 47–54 Occurrence Handle10.1021/pr015509n Occurrence Handle12643526
J. Li H. Steen S. P. Gygi (2003) ArticleTitleProtein profiling with cleavable isotope-coded affinity Tag (cICAT) reagents: the yeast salinity stress response Mol. Cell Proteomics 2 1198–1204 Occurrence Handle10.1074/mcp.M300070-MCP200 Occurrence Handle14506205
K. J. Reynolds X. Yao C. Fenselau (2002) ArticleTitleProteolytic 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent J. Proteome Res. 1 27–33 Occurrence Handle10.1021/pr0100016 Occurrence Handle12643523
A. Staes H. Demol J. Damme ParticleVan L. Martens J. Vandekerckhove K. Gevaert (2004) ArticleTitleGlobal differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18 J. Proteome Res. 3 786–791 Occurrence Handle10.1021/pr049956p Occurrence Handle15359732
K. Gevaert M. Goethals L. Martens J. Damme ParticleVan A. Staes G. R. Thomas J. Vandekerckhove (2003) ArticleTitleExploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides Nat. Biotechnol. 21 566–569 Occurrence Handle10.1038/nbt810 Occurrence Handle12665801
Pappin, D. J., Ross, P. L., Purkayastha, S., Haley, J. D., Peltier, J., and Zieske, L. R. (2004) Protein and biomarker quantitation using iTRAQ reagents, a novel set of multiplexed amine-specific tagging reagents. In: Abstract Book of the 6th Siena Meeting from Genome to Proteome: Biomarker Discovery & Proteome imaging, Siena, Italy, p. 67.
Hamon, C., Kuhn, K., Kienle, S., Schäfer, J., and Schwarz, J. (2004) Tandem mass tags–a novel strategy for differential quantitative analysis of complex proteomes. In: Abstract Book of the 6th Siena Meeting from Genome to Proteome: Biomarker Discovery Proteome imaging, Siena, Italy, p. 68.
A. Thompson J. Schafer K. Kuhn S. Kienle J. Schwarz G. Schmidt R. Johnstone T. Neumann C. Hamon (2003) ArticleTitleTandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 75 1895–1904 Occurrence Handle10.1021/ac0262560 Occurrence Handle12713048
H. Zhang W. Yan R. Aebersold (2004) ArticleTitleChemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes Curr. Opin. Chem. Biol. 8 66–75 Occurrence Handle10.1016/j.cbpa.2003.12.001 Occurrence Handle15036159
D. M. Desiderio X. Zhu (1998) ArticleTitleQuantitative analysis of methionine enkephalin and beta-endorphin in the pituitary by liquid secondary ion mass spectrometry and tandem mass spectrometry J. Chromatogr. A 794 85–96 Occurrence Handle10.1016/S0021-9673(97)00670-5 Occurrence Handle9491558
P. Bottari R. Aebersold F. Turecek M. H. Gelb (2004) ArticleTitleDesign and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures Bioconjug. Chem. 15 380–388 Occurrence Handle10.1021/bc034174s Occurrence Handle15025535
Y. Lu P. Bottari F. Turecek R. Aebersold M. H. Gelb (2004) ArticleTitleAbsolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags Anal. Chem. 76 4104–4111 Occurrence Handle10.1021/ac049905b Occurrence Handle15253649
S. A. Gerber J. Rush O. Stemman M. W. Kirschner S. P. Gygi (2003) ArticleTitleAbsolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proc. Natl. Acad. Sci. USA 100 6940–6945 Occurrence Handle10.1073/pnas.0832254100 Occurrence Handle12771378
C. Stannard P. Lehenkari J. Godovac-Zimmermann (2003) ArticleTitleFunctional diversity of endothelin pathways in human lung fibroblasts may be based on structural diversity of the endothelin receptors Biochemistry 42 13909–13918 Occurrence Handle10.1021/bi0354132 Occurrence Handle14636059
C. Stannard V. Soskic J. Godovac-Zimmermann (2003) ArticleTitleRapid changes in the phosphoproteome show diverse cellular responses following stimulation of human lung fibroblasts with endothelin-1 Biochemistry 42 13,919–13928
Hinsby, A. M., Olsen, J. V., and Mann, M. (2004) Tyrosine phosphoproteomics of FGF signaling – a role for insulin receptor substrate-4. J. Biol. Chem. DOI 10.1074/jbc.
V. Soskic M. Gorlach S. Poznanovic F. D. Boehmer J. Godovac-Zimmermann (1999) ArticleTitleFunctional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor Biochemistry 38 1757–1764 Occurrence Handle10.1021/bi982093r Occurrence Handle10026255
M. Gronborg T. Z. Kristiansen A. Stensballe J. S. Andersen O. Ohara M. Mann O. N. Jensen A. Pandey (2002) ArticleTitleA mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate Mol. Cell Proteomics 1 517–527 Occurrence Handle10.1074/mcp.M200010-MCP200 Occurrence Handle12239280
K. A. Mowen M. David (2001) ArticleTitleAnalysis of protein arginine methylation and protein arginine-methyltransferase activity Sci. STKE 93 31
S. B. Ficarro M. L. McCleland P. T. Stukenberg D. J. Burke M. M. Ross J. Shabanowitz D. F. Hunt F. M. White (2002) ArticleTitlePhosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 20 301–305 Occurrence Handle10.1038/nbt0302-301 Occurrence Handle11875433
T. S. Nuhse A. Stensballe O. N. Jensen S. C. Peck (2003) ArticleTitleLarge-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry Mol. Cell Proteomics 2 1234–1243 Occurrence Handle10.1074/mcp.T300006-MCP200 Occurrence Handle14506206
J. Bunkenborg B. J. Pilch A. V. Podtelejnikov J. R. Wisniewski (2004) ArticleTitleScreening for N-glycosylated proteins by liquid chromatography mass spectrometry Proteomics 4 454–465 Occurrence Handle10.1002/pmic.200300556 Occurrence Handle14760718
H. Kaji H. Saito Y. Yamauchi T. Shinkawa M. Taoka J. Hirabayashi K. Kasai N. Takahashi T. Isobe (2003) ArticleTitleLectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins Nat. Biotechnol. 21 667–672 Occurrence Handle10.1038/nbt829 Occurrence Handle12754521
J. Zaia (2004) ArticleTitleMass spectrometry of oligosaccharides Mass Spectrom. Rev. 23 161–227 Occurrence Handle10.1002/mas.10073 Occurrence Handle14966796
M. B. Goshe T. P. Conrads E. A. Panisko N. H. Angell T. D. Veenstra R. D. Smith (2001) ArticleTitlePhosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses Anal. Chem. 73 2578–2586 Occurrence Handle10.1021/ac010081x Occurrence Handle11403303
Y. Oda T. Nagasu B. T. Chait (2001) ArticleTitleEnrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 19 379–382 Occurrence Handle10.1038/86783 Occurrence Handle11283599
H. Zhou J. D. Watts R. Aebersold (2001) ArticleTitleA systematic approach to the analysis of protein phosphorylation Nat. Biotechnol. 19 375–378 Occurrence Handle10.1038/86777 Occurrence Handle11283598
H. Steen M. Mann (2002) ArticleTitleA new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode J. Am. Soc. Mass Spectrom. 13 996–1003 Occurrence Handle10.1016/S1044-0305(02)00415-4 Occurrence Handle12216740
L. Wells K. Vosseller R. N. Cole J. M. Cronshaw M. J. Matunis G. W. Hart (2002) ArticleTitleMapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications Mol. Cell Proteomics 1 791–804 Occurrence Handle10.1074/mcp.M200048-MCP200 Occurrence Handle12438562
H. Zhang X. J. Li D. B. Martin R. Aebersold (2003) ArticleTitleIdentification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry Nat. Biotechnol. 21 660–666 Occurrence Handle10.1038/nbt827 Occurrence Handle12754519
G. Nikov V. Bhat J. S. Wishnok S. R. Tannenbaum (2003) ArticleTitleAnalysis of nitrated proteins by nitrotyrosine-specific affinity probes and mass spectrometry Anal. Biochem. 320 214–222 Occurrence Handle10.1016/S0003-2697(03)00359-2 Occurrence Handle12927827
T. Kuncewicz E. A. Sheta I. L. Goldknopf B. C. Kone (2003) ArticleTitleProteomic analysis of S-nitrosylated proteins in mesangial cells Mol. Cell Proteomics 2 156–163 Occurrence Handle10.1074/mcp.M300003-MCP200 Occurrence Handle12671063
A. Martinez-Ruiz S. Lamas (2004) ArticleTitleDetection and proteomic identification of S-nitrosylated proteins in endothelial cells Arch. Biochem. Biophys. 423 192–199 Occurrence Handle10.1016/j.abb.2003.12.006 Occurrence Handle14871481
T. P. Conrads H. J. Issaq T. D. Veenstra (2002) ArticleTitleNew tools for quantitative phosphoproteome analysis Biochem. Biophys. Res. Commun. 290 885–890 Occurrence Handle10.1006/bbrc.2001.6275 Occurrence Handle11798155
O. N. Jensen (2004) ArticleTitleModification-specific proteomics: characterization of post-translational modifications by mass spectrometry Curr. Opin. Chem. Biol. 8 33–41 Occurrence Handle10.1016/j.cbpa.2003.12.009 Occurrence Handle15036154
M. Mann O. N. Jensen (2003) ArticleTitleProteomic analysis of post-translational modifications Nat. Biotechnol. 21 255–261 Occurrence Handle10.1038/nbt0303-255 Occurrence Handle12610572
R. A. Zubarev N. L. Kelleher F. W. McLafferty (1998) ArticleTitleElectron capture dissociation of multiply charged protein cations. A nonergodic process J. Am. Chem. Soc. 120 3265–3266 Occurrence Handle10.1021/ja973478k
S. D. Shi M. E. Hemling S. A. Carr D. M. Horn I. Lindh F. W. McLafferty (2001) ArticleTitlePhosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry Anal. Chem. 73 19–22 Occurrence Handle10.1021/ac000703z Occurrence Handle11195502
S. K. Sze Y. Ge H. Oh F. W. McLafferty (2003) ArticleTitlePlasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry Anal. Chem. 75 1599–1603 Occurrence Handle10.1021/ac020446t Occurrence Handle12705591
R. A. Zubarev (2004) ArticleTitleElectron-capture dissociation tandem mass spectrometry Curr. Opin. Biotechnol. 15 12–16 Occurrence Handle10.1016/j.copbio.2003.12.002 Occurrence Handle15102460
P. Chaurand R. M. Caprioli (2002) ArticleTitleDirect profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry Electrophoresis 23 3125–3135 Occurrence Handle10.1002/1522-2683(200209)23:18<3125::AID-ELPS3125>3.0.CO;2-# Occurrence Handle12298084
K. Yanagisawa Y. Shyr B. J. Xu P. P. Massion P. H. Larsen B. C. White J. R. Roberts M. Edgerton A. Gonzalez S. Nadaf J. H. Moore R. M. Caprioli D. P. Carbone (2003) ArticleTitleProteomic patterns of tumour subsets in non-small-cell lung cancer Lancet 362 433–439 Occurrence Handle10.1016/S0140-6736(03)14068-8 Occurrence Handle12927430
R. W. Garden J. V. Sweedler (2000) ArticleTitleHeterogeneity within MALDI samples as revealed by mass spectrometric imaging Anal. Chem. 72 30–36 Occurrence Handle10.1021/ac9908997 Occurrence Handle10655631
B. Spengler M. Hubert (2002) ArticleTitleScanning microprobe matrix-assisted laser desorption ionization (SMALDI) mass spectrometry: instrumentation for sub-micrometer resolved LDI and MALDI surface analysis J. Am. Soc. Mass Spectrom. 13 735–748 Occurrence Handle10.1016/S1044-0305(02)00376-8 Occurrence Handle12056573
M. Stoeckli T. B. Farmer R. M. Caprioli (1999) ArticleTitleAutomated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument J. Am. Soc. Mass Spectrom. 10 67–71 Occurrence Handle10.1016/S1044-0305(98)00126-3 Occurrence Handle9888186
P. Chaurand S. A. Schwartz R. M. Caprioli (2004) ArticleTitleAssessing protein patterns in disease using imaging mass spectrometry J. Proteome Res. 3 245–252 Occurrence Handle10.1021/pr0341282 Occurrence Handle15113100
P. J. Todd T. G. Schaaff P. Chaurand R. M. Caprioli (2001) ArticleTitleOrganic ion imaging of biological tissue with secondary ion mass spectrometry and matrix-assisted laser desorption/ionization J. Mass Spectrom. 36 355–369 Occurrence Handle10.1002/jms.153 Occurrence Handle11333438
S. L. Luxembourg T. H. Mize L. A. McDonnell R. M. Heeren (2004) ArticleTitleHigh-spatial resolution mass spectrometric imaging of peptide and protein distributions on a surface Anal. Chem. 76 5339–5344 Occurrence Handle10.1021/ac049692q Occurrence Handle15362890
B. W. Schueler (1992) ArticleTitleMicroscope imaging by time-of-flight secondary ion mass spectrometry Microsc. Microanal. Microstruct. 3 119–139
A. Oelsner O. Schmidt M. Schicketanz M. Klais G. Schönhense V. Mergel O. Jagutzki H. Schmidt-Böcking (2001) ArticleTitleMicrospectroscopy and imaging using a delay line detector in time-of-flight photoemission microscopy Rev. Sci. Instrum. 72 3968–3974 Occurrence Handle10.1063/1.1405781
S. A. Beausoleil M. Jedrychowski D. Schwartz J. E. Elias J. Villen J. Li M. A. Cohn L. C. Cantley S. P. Gygi (2004) ArticleTitleLarge-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. USA 101 12130–12135 Occurrence Handle10.1073/pnas.0404720101 Occurrence Handle15302935
M. J. MacCoss W. H. McDonald A. Saraf R. Sadygov J. M. Clark J. J. Tasto K. L. Gould D. Wolters M. Washburn A. Weiss J. I. Clark J. R. Yates SuffixIII (2002) ArticleTitleShotgun identification of protein modifications from protein complexes and lens tissue Proc. Natl. Acad. Sci. USA 99 7900–7905 Occurrence Handle10.1073/pnas.122231399 Occurrence Handle12060738
J. E. Dumont S. Dremier I. Pirson C. Maenhaut (2002) ArticleTitleCross signaling, cell specificity, and physiology Am. J. Physiol. Cell Physiol. 283 C2–28 Occurrence Handle12055068
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Guerrera, I.C., Kleiner, O. Application of Mass Spectrometry in Proteomics. Biosci Rep 25, 71–93 (2005). https://doi.org/10.1007/s10540-005-2849-x
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DOI: https://doi.org/10.1007/s10540-005-2849-x