Abstract
Background: Mass spectrometry is a tool used in analytical chemistry to identify components in a chemical compound and it is of tremendous importance in the field of biology for high throughput analysis of biomolecules, among which protein is of great interest.
Objective: Advancement in proteomics based on mass spectrometry has led the way to quantify multiple protein complexes, and proteins interactions with DNA/RNA or other chemical compounds which is a breakthrough in the field of bioinformatics.
Methods: Many new technologies have been introduced in electrospray ionization (ESI) and Matrixassisted Laser Desorption/Ionization (MALDI) techniques which have enhanced sensitivity, resolution and many other key features for the characterization of proteins.
Results: The advent of ambient mass spectrometry and its different versions like Desorption Electrospray Ionization (DESI), DART and ELDI has brought a huge revolution in proteomics research. Different imaging techniques are also introduced in MS to map proteins and other significant biomolecules. These drastic developments have paved the way to analyze large proteins of >200kDa easily.
Conclusion: Here, we discuss the recent advancement in mass spectrometry, which is of great importance and it could lead us to further deep analysis of the molecules from different perspectives and further advancement in these techniques will enable us to find better ways for prediction of molecules and their behavioral properties.
Keywords: Mass spectrometry, ionization methods, proteomics, DART, MALDI, dispersion samples.
Graphical Abstract
[1]
Gstaiger, M.; Aebersold, R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet., 2009, 10, 617-627.
[3]
Blaum, K.; Litvinov, Y.A. 100 years of mass spectrometry. Int. J. Mass Spectrom., 2013, 349-350, 1-276.
[4]
Angel, T.E.; Aryal, U.K.; Hengel, S.M.; Baker, E.S.; Kelly, R.T.; Robinson, E.W.; Smith, R.D. Mass spectrometry-based proteomics: Existing capabilities and future directions. Chem. Soc. Rev., 2012, 41, 3912-3928.
[5]
Harkewicz, R.; Dennis, E.A. Applications of mass spectrometry to lipids and membranes. Annu. Rev. Biochem., 2011, 80, 301-325.
[6]
Kocher, T.; Superti-Furga, G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods, 2007, 4, 807-815.
[8]
Schulze, W.X.; Usadel, B. Quantitation in mass-spectrometry-based proteomics. Annu. Rev. Plant Biol., 2010, 61, 491-516.
[9]
Bensimon, A.; Heck, A.J.; Aebersold, R. Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem., 2012, 81, 379-405.
[10]
Hsu, F.J.; Liu, T.L.; Laskar, A.H.; Shiea, J.; Huang, M.Z. Gravitational sampling electrospray ionization mass spectrometry for real-time reaction monitoring. Rapid Commun. Mass Spectrom., 2014, 28, 1979-1986.
[11]
Snijder, J.; Heck, A.J. Analytical approaches for size and mass analysis of large protein assemblies. Annu. Rev. Anal. Chem., (Palo Alto Calif) 2014, 7, 43-64.
[13]
Joyner, J.C.; Keuper, K.D.; Cowan, J.A. Analysis of RNA cleavage by MALDI-TOF mass spectrometry. Nucleic Acids Res., 2013, 41, e2.
[14]
Bantscheff, M.; Lemeer, S.; Savitski, M.M.; Kuster, B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem., 2012, 404, 939-965.
[15]
Bauer, A.; Kuster, B. Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes. Eur. J. Biochem., 2003, 270, 570-578.
[16]
Walther, T.C.; Mann, M. Mass spectrometry-based proteomics in cell biology. J. Cell Biol., 2010, 190, 491-500.
[17]
Nesvizhskii, A.I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem., 2003, 75, 4646-4658.
[18]
Sauer, S.; Freiwald, A.; Maier, T.; Kube, M.; Reinhardt, R.; Kostrzewa, M.; Geider, K. Classification and identification of bacteria by mass spectrometry and computational analysis. PLoS One, 2008, 3, e2843.
[19]
Pedrioli, P.G.; Eng, J.K.; Hubley, R.; Vogelzang, M.; Deutsch, E.W.; Raught, B.; Pratt, B.; Nilsson, E.; Angeletti, R.H.; Apweiler, R.; Cheung, K.; Costello, C.E.; Hermjakob, H.; Huang, S.; Julian, R.K.; Kapp, E.; McComb, M.E.; Oliver, S.G.; Omenn, G.; Paton, N.W.; Simpson, R.; Smith, R.; Taylor, C.F.; Zhu, W.; Aebersold, R. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol., 2004, 22, 1459-1466.
[20]
Lamond, A.; Uhlen, M.; Horning, S.; Makarov, A.; Robinson, C.V.; Serrano, L.; Hartl, F.U.; Baumeister, W.; Werenskiold, A.K.; Andersen, J.S.; Vorm, O.; Linial, M.; Aebersold, R.; Mann, M. Advancing cell biology through proteomics in space and time (prospects). Mol. Cell Proteomics, 2012. 11, O112.017731.
[21]
Babu, M.; Kagan, O.; Guo, H.; Greenblatt, J.; Emili, A. Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J. Vis. Exp., 2012, 69, 4057.
[22]
Mann, M.; Hendrickson, R.C.; Pandey, A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem., 2001, 70, 437-473.
[23]
Konermann, L.; Ahadi, E.; Rodriguez, A.D.; Vahidi, S. Unraveling the mechanism of electrospray ionization. Anal. Chem., 2013, 85, 2-9.
[24]
Huang, M.Z.; Hsu, H.J.; Lee, J.Y.; Jeng, J.; Shiea, J. Direct protein detection from biological media through electrospray-assisted laser desorption ionization/mass spectrometry. J. Proteome Res., 2006, 5, 1107-1116.
[25]
Yates, J.R.; Ruse, C.I.; Nakorchevsky, A. Proteomics by mass spectrometry: Approaches, advances, and applications. Annu. Rev. Biomed. Eng., 2009, 11, 49-79.
[26]
Cox, J.; Hein, M.Y.; Luber, C.A.; Paron, I.; Nagaraj, N.; Mann, M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics, 2014, 13, 2513-2526.
[27]
Dason, S.R.P.; Batruch, I.; Smith, C.R.; Diamandis, E.P. Evaluation of sieve as a label-free mass spectrometry protein quantification method. J. Undergrad. Life Sci., 2009, 3, 33-35.
[28]
Standard, G.; Processing, Q.D. MultiQuant TM software 2 . 0 for targeted protein / peptide quantification. Sciex, 1-5.
[29]
Nilsson, T.; Mann, M.; Aebersold, R.; Yates, J.R.; Bairoch, A.; Bergeron, J.J. Mass spectrometry in high-throughput proteomics: Ready for the big time. Nat. Methods, 2010, 7, 681-685.
[30]
Cote, R.G.; Griss, J.; Dianes, J.A.; Wang, R.; Wright, J.C.; van den Toorn, H.W.; van Breukelen, B.; Heck, A.J.; Hulstaert, N.; Martens, L.; Reisinger, F.; Csordas, A.; Ovelleiro, D.; Perez-Rivevol, Y.; Barsnes, H.; Hermjakob, H.; Vizcaino, J.A. The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the proteomexchange consortium. Mol. Cell. Proteomics, 2012, 11, 1682-1689.
[31]
Vizcaino, J.A.; Deutsch, E.W.; Wang, R.; Csordas, A.; Reisinger, F.; Rios, D.; Dianes, J.A.; Sun, Z.; Farrah, T.; Bandeira, N.; Binz, P.A.; Xenarios, I.; Eisenacher, M.; Mayer, G.; Gatto, L.; Campos, A.; Chalkley, R.J.; Kraus, H.J.; Albar, J.P.; Martinez-Bartolome, S.; Apweiler, R.; Omenn, G.S.; Martens, L.; Jones, A.R.; Hermjakob, H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol., 2014, 32, 223-226.
[32]
Chernushevich, I.V.; Loboda, A.V.; Thomson, B.A. An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom., 2001, 36, 849-865.
[33]
Makarov, A.; Denisov, E.; Kholomeev, A.; Balschun, W.; Lange, O.; Strupat, K.; Horning, S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem., 2006, 78, 2113-2120.
[35]
Mandal, M.K.; Chen, L.C.; Hashimoto, Y.; Yu, Z.; Hiraoka, K. Detection of biomolecules from solutions with high concentration of salts using probe electrospray and nano-electrospray ionization mass spectrometry. Anal. Methods, 2010, 2, 1905-1912.
[36]
Heck, A.J.; Van Den Heuvel, R.H. Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev., 2004, 23, 368-389.
[37]
Kebarle, P.; Verkerk, U.H. Electrospray: From ions in solution to ions in the gas phase, what we know now. Mass Spectrom. Rev., 2009, 28, 898-917.
[38]
Banerjee, S.; Mazumdar, S. Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. Int. J. Anal. Chem., 2012, 2012, 282574.
[39]
Hilton, G.R.; Benesch, J.L. Two decades of studying non-covalent biomolecular assemblies by means of electrospray ionization mass spectrometry. J. Soc. Interface, 2012, 9, 801-816.
[40]
Hu, B.; So, P.K.; Chen, H.; Yao, Z.P. Electrospray ionization using wooden tips. Anal. Chem., 2011, 83, 8201-8207.
[41]
Dreisewerd, K. Recent methodological advances in MALDI mass spectrometry. Anal. Bioanal. Chem., 2014, 406, 2261-2278.
[42]
Croxatto, A.; Prod’hom, G.; Greub, G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol. Rev., 2012, 36, 380-407.
[43]
Guerrera, I.C.; Kleiner, O. Application of mass spectrometry in proteomics. Biosci. Rep., 2005, 25, 71-93.
[44]
Madler, S.; Boeri, E.E.; Zenobi, R. MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules. Top. Curr. Chem., 2013, 331, 1-36.
[45]
Yao, Z.P. Characterization of proteins by ambient mass spectrometry. Mass Spectrom. Rev., 2012, 31, 437-447.
[46]
Wiseman, J.M.; Laughlin, B.C. Desorption electrospray ionization (DESI) mass spectrometry: A brief introduction and overview. Prosolia, Inc., Indianapolis, In USA pp. 11-14.
[47]
Monge, M.E.; Harris, G.A.; Dwivedi, P.; Fernandez, F.M. Mass spectrometry: recent advances in direct open air surface sampling/ionization. Chem. Rev., 2013, 113, 2269-2308.
[48]
Thunig, J.; Hansen, S.H.; Janfelt, C. Analysis of secondary plant metabolites by indirect desorption electrospray ionization imaging mass spectrometry. Anal. Chem., 2011, 83, 3256-3259.
[49]
Ferguson, C.N.; Benchaar, S.A.; Miao, Z.; Loo, J.A.; Chen, H. Direct ionization of large proteins and protein complexes by desorption electrospray ionization-mass spectrometry. Anal. Chem., 2011, 83, 6468-6473.
[50]
Takats, Z.; Wiseman, J.M.; Gologan, B.; Cooks, R.G. Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science, 2004, 306, 471-473.
[51]
Harris, G.A.; Galhena, A.S.; Fernandez, F.M. Ambient sampling/ionization mass spectrometry: applications and current trends. Anal. Chem., 2011, 83, 4508-4538.
[52]
Friia, M.; Legros, V.; Tortajada, J.; Buchmann, W. Desorption electrospray ionization - orbitrap mass spectrometry of synthetic polymers and copolymers. J. Mass Spectrom., 2012, 47, 1023-1033.
[53]
Chernetsova, E.S.; Morlock, G.E. Ambient desorption ionization mass spectrometry (DART, DESI) and its bioanalytical applications. Bioanal. Rev., 2011, 3, 1-9.
[54]
Hsu, C.C.; White, N.M.; Hayashi, M.; Lin, E.C.; Poon, T.; Banerjee, I.; Chen, J.; Pfaff, S.L.; Macagno, E.R.; Dorrestein, P.C. Microscopy ambient ionization top-down mass spectrometry reveals developmental patterning. Proc. Natl. Acad. Sci. USA, 2013, 110, 14855-14860.
[55]
Kononikhin, A.; Huang, M.Z.; Popov, I.; Kostyukevich, Y.; Kukaev, E.; Boldyrev, A.; Spasskiy, A.; Leypunskiy, I.; Shiea, J.; Nikolaev, E. Signal enhancement in electrospray laser desorption/ionization mass spectrometry by using a black oxide-coated metal target and a relatively low laser fluence. Eur. J. Mass Spectrom. , 2013, 19, 247-252.
[56]
Robichaud, G.; Barry, J.A.; Garrard, K.P.; Muddiman, D.C. Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) imaging source coupled to a FT-ICR mass spectrometer. J. Am. Soc. Mass Spectrom., 2013, 24, 92-100.
[57]
Seeley, E.H.; Caprioli, R.M. Molecular imaging of proteins in tissues by mass spectrometry. Proc. Natl. Acad. Sci. USA, 2008, 105, 18126-18131.
[58]
McDonnell, L.A.; Heeren, R.M. Imaging mass spectrometry. Mass Spectrom. Rev., 2007, 26, 606-643.
[59]
Amstalden van Hove, E.R.; Smith, D.F.; Heeren, R.M. A concise review of mass spectrometry imaging. J. Chromatogr. A, 2010, 1217, 3946-3954.
[60]
Rubakhin, S.S.; Jurchen, J.C.; Monroe, E.B.; Sweedler, J.V. Imaging mass spectrometry: Fundamentals and applications to drug discovery. Drug Discov. Today, 2005, 10, 823-837.
[61]
Groseclose, M.R.; Massion, P.P.; Chaurand, P.; Caprioli, R.M. High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics, 2008, 8, 3715-3724.
[62]
Walch, A.; Rauser, S.; Deininger, S.O.; Hofler, H. MALDI imaging mass spectrometry for direct tissue analysis: A new frontier for molecular histology. Histochem. Cell Biol., 2008, 130, 421-434.
[63]
Cornett, D.S.; Reyzer, M.L.; Chaurand, P.; Caprioli, R.M. MALDI imaging mass spectrometry: Molecular snapshots of biochemical systems. Nat. Methods, 2007, 4, 828-833.
[64]
Douglass, K.A.; Ifa, D.R.; Venter, A.R. Technologies and principles of mass spectral imaging. In: Moyer, B.; Cheruvu, N.; Hu, T.C.; Eds Pharmaco-imaging in drug and biologics development. Adv. Pharmaceut. Sci. Series; vol. 8, Springer, New York, NY, USA . , 2014.
[65]
Kaspar, S.; Peukert, M.; Svatos, A.; Matros, A.; Mock, H.P. MALDI-imaging mass spectrometry-an emerging technique in plant biology. Proteomics, 2011, 11, 1840-1850.
[66]
Vickerman, J.C. Molecular imaging and depth profiling by mass spectrometry-SIMS, MALDI or DESI? Analyst , 2011, 136, 2199-2217.
[67]
Watrous, J.D.; Alexandrov, T.; Dorrestein, P.C. The evolving field of imaging mass spectrometry and its impact on future biological research. J. Mass Spectrom., 2011, 46, 209-222.
[68]
Seeley, E.H.; Caprioli, R.M. 3D imaging by mass spectrometry: a new frontier. Anal. Chem., 2012, 84, 2105-2110.
[69]
Ifa, D.R.; Wiseman, J.M.; Song, Q.; Cooks, R.G. Development of capabilities for imaging mass spectrometry under ambient conditions with desorption electrospray ionization (DESI). Int. J. Mass Spectrom., 2007, 259, 8-15.
[70]
Chughtai, K.; Heeren, R.M. Mass spectrometric imaging for biomedical tissue analysis. Chem. Rev., 2010, 110, 3237-3277.
[71]
Calligaris, D.; Caragacianu, D.; Liu, X.; Norton, I.; Thompson, C.J.; Richardson, A.L.; Golshan, M.; Easterling, M.L.; Santagata, S.; Dillon, D.L.; Agar, N.Y.R. Application of desorption electrospray ionization mass spectrometry imaging in breast cancer margin analysis. PNAS, 2014, 111, 15184-15189.
[72]
Kerian, K.S.; Jarmusch, A.K.; Pirro, V.; Koch, M.O.; Masterson, T.A.; Cooks, R.G. Differentiation of prostate cancer from normal tissue in radical prostatectomy specimens by desorption electrospray ionization and touch spray ionization mass spectrometry. Analyst , 2015, 140, 1090-1098.
Related Journals
Related Books
Industrial Applications of Soil Microbes
Industrial Applications of Soil Microbes
Algal Biotechnology for Fuel Applications
Biopolymers Towards Green and Sustainable Development
Terpenoids: Recent Advances in Extraction, Biochemistry and Biotechnology
Environmental Microbiology: Advanced Research and Multidisciplinary Applications
Biomarkers in Medicine
Industrial Applications of Soil Microbes
Recent Advances in Biotechnology
Sustainable Utilization of Fungi in Agriculture and Industry
Article Metrics
60
9
1
1