Generic placeholder image

Current Protein & Peptide Science

Editor-in-Chief

ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Review Article

Mass Spectrometric (MS) Analysis of Proteins and Peptides

Author(s): Madhuri Jayathirtha, Emmalyn J. Dupree, Zaen Manzoor, Brianna Larose, Zach Sechrist, Anca-Narcisa Neagu, Brindusa Alina Petre and Costel C. Darie*

Volume 22, Issue 2, 2021

Published on: 26 July, 2020

Page: [92 - 120] Pages: 29

DOI: 10.2174/1389203721666200726223336

Price: $65

conference banner
Abstract

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

Keywords: Mass spectrometry (MS), proteins, peptides, PTMs, ESI-MS, MALDI-MS, MALDI-MSI.

Graphical Abstract
[1]
Woods, A.G.; Sokolowska, I.; Ngounou Wetie, A.G.; Channaveerappa, D.; Dupree, E.J.; Jayathirtha, M.; Aslebagh, R.; Wormwood, K.L.; Darie, C.C. Mass Spectrometry for Proteomics-Based Investigation. Adv. Exp. Med. Biol., 2019, 1140, 1-26.
[http://dx.doi.org/10.1007/978-3-030-15950-4_1 ] [PMID: 31347039]
[2]
Woods, A.G.; Sokolowska, I.; Ngounou Wetie, A.G.; Wormwood, K.; Aslebagh, R.; Patel, S.; Darie, C.C. Mass spectrometry for proteomics-based investigation. Adv. Exp. Med. Biol., 2014, 806, 1-32.
[http://dx.doi.org/10.1007/978-3-319-06068-2_1 ] [PMID: 24952176]
[3]
Aslebagh, R.; Channaveerappa, D.; Arcaro, K.F.; Darie, C.C. Comparative two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of human milk to identify dysregulated proteins in breast cancer. Electrophoresis, 2018.
[http://dx.doi.org/10.1002/elps.201800025 ] [PMID: 29756217]
[4]
Channaveerappa, D.; Lux, J.C.; Wormwood, K.L.; Heintz, T.A.; McLerie, M.; Treat, J.A.; King, H.; Alnasser, D.; Goodrow, R.J.; Ballard, G.; Decker, R.; Darie, C.C.; Panama, B.K. Atrial electrophysiological and molecular remodelling induced by obstructive sleep apnoea. J. Cell. Mol. Med., 2017, 21(9), 2223-2235.
[http://dx.doi.org/10.1111/jcmm.13145 ] [PMID: 28402037]
[5]
Kendrick, N.; Darie, C.C.; Hoelter, M.; Powers, G.; Johansen, J. 2D SDS PAGE in Combination with Western Blotting and Mass Spectrometry Is a Robust Method for Protein Analysis with Many Applications. Adv. Exp. Med. Biol., 2019, 1140, 563-574.
[http://dx.doi.org/10.1007/978-3-030-15950-4_33 ] [PMID: 31347071]
[6]
Ngounou Wetie, A.G.; Wormwood, K.L.; Russell, S.; Ryan, J.P.; Darie, C.C.; Woods, A.G. A Pilot Proteomic Analysis of Salivary Biomarkers in Autism Spectrum Disorder. Autism Res., 2015, 8(3), 338-350.
[http://dx.doi.org/10.1002/aur.1450 ] [PMID: 25626423]
[7]
Virág, D. Current Trends in the Analysis of Post-translational Modifications. Chromatographia, 2020, 83(1), 1-10.
[http://dx.doi.org/10.1007/s10337-019-03796-9]
[8]
Mädler, S.; Barylyuk, K.; Boeri Erba, E.; Nieckarz, R.J.; Zenobi, R. Compelling advantages of negative ion mode detection in high-mass MALDI-MS for homomeric protein complexes. J. Am. Soc. Mass Spectrom., 2012, 23(2), 213-224.
[http://dx.doi.org/10.1007/s13361-011-0274-x ] [PMID: 22131225]
[9]
Crecelius, A.C.; Schubert, U.S.; von Eggeling, F. MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage. Analyst (Lond.), 2015, 140(17), 5806-5820.
[http://dx.doi.org/10.1039/C5AN00990A ] [PMID: 26161715]
[10]
Fenn, J.B.; Mann, M.; Meng, C.K.; Wong, S.F.; Whitehouse, C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science, 1989, 246(4926), 64-71.
[http://dx.doi.org/10.1126/science.2675315 ] [PMID: 2675315]
[11]
Kaufmann, R. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry: a novel analytical tool in molecular biology and biotechnology. J. Biotechnol., 1995, 41(2-3), 155-175.
[http://dx.doi.org/10.1016/0168-1656(95)00009-F ] [PMID: 7654348]
[12]
Chaurand, P.; Luetzenkirchen, F.; Spengler, B. Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom., 1999, 10(2), 91-103.
[http://dx.doi.org/10.1016/S1044-0305(98)00145-7 ] [PMID: 9926404]
[13]
Mnatsakanyan, R.; Shema, G.; Basik, M.; Batist, G.; Borchers, C.H.; Sickmann, A.; Zahedi, R.P. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev. Proteomics, 2018, 15(6), 515-535.
[http://dx.doi.org/10.1080/14789450.2018.1483340 ] [PMID: 29893147]
[14]
Iimuro, R.; Takayama, M. Analysis of Flexibility of Proteins by means of Positive and Negative Ion MALDI In-Source Decay Mass Spectrometry. Mass Spectrom. (Tokyo), 2014, 3(Spec Iss), S0023-S0023.
[http://dx.doi.org/10.5702/massspectrometry.S0023 ] [PMID: 26819895]
[15]
Liu, Z.; Schey, K.L. Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis. J. Am. Soc. Mass Spectrom., 2005, 16(4), 482-490.
[http://dx.doi.org/10.1016/j.jasms.2004.12.018 ] [PMID: 15792717]
[16]
Alomirah, H.F.; Alli, I.; Konishi, Y. Applications of mass spectrometry to food proteins and peptides. J. Chromatogr. A, 2000, 893(1), 1-21.
[http://dx.doi.org/10.1016/S0021-9673(00)00745-7 ] [PMID: 11043583]
[17]
Bucknall, M.; Fung, K.Y.C.; Duncan, M.W. Practical quantitative biomedical applications of MALDI-TOF mass spectrometry. J. Am. Soc. Mass Spectrom., 2002, 13(9), 1015-1027.
[http://dx.doi.org/10.1016/S1044-0305(02)00426-9 ] [PMID: 12322949]
[18]
Gao, J.; Cassady, C.J. Negative ion production from peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 2008, 22(24), 4066-4072.
[http://dx.doi.org/10.1002/rcm.3818 ] [PMID: 19021134]
[19]
Ho, C.S.; Lam, C.W.; Chan, M.H.; Cheung, R.C.; Law, L.K.; Lit, L.C.; Ng, K.F.; Suen, M.W.; Tai, H.L. Electrospray ionisation mass spectrometry: principles and clinical applications. Clin. Biochem. Rev., 2003, 24(1), 3-12. [PMID: 18568044
[20]
Katsanovskaja, K.; Driver, T.; Pipkorn, R.; Edelson-Averbukh, M. Negative Ion Mode Collision-Induced Dissociation for Analysis of Protein Arginine Methylation. J. Am. Soc. Mass Spectrom., 2019, 30(7), 1229-1241.
[http://dx.doi.org/10.1007/s13361-019-02176-9 ] [PMID: 30915654]
[21]
Hou, J.; Xie, Z.; Xue, P.; Cui, Z.; Chen, X.; Li, J.; Cai, T.; Wu, P.; Yang, F. Enhanced MALDI-TOF MS analysis of phosphopeptides using an optimized DHAP/DAHC matrix. J. Biomed. Biotechnol., 2010, 2010, 759690-759690.
[http://dx.doi.org/10.1155/2010/759690 ] [PMID: 20339515]
[22]
Xu, C-F.; Lu, Y.; Ma, J.; Mohammadi, M.; Neubert, T.A. Identification of phosphopeptides by MALDI Q-TOF MS in positive and negative ion modes after methyl esterification. Mol. Cell. Proteomics, 2005, 4(6), 809-818.
[http://dx.doi.org/10.1074/mcp.T400019-MCP200 ] [PMID: 15753120]
[23]
Pomastowski, P.; Buszewski, B. Complementarity of Matrix- and Nanostructure-Assisted Laser Desorption/Ionization Approaches. Nanomaterials (Basel), 2019, 9(2), 260.
[http://dx.doi.org/10.3390/nano9020260 ] [PMID: 30769830]
[24]
Ding, F.; Qian, Y.; Deng, Z.; Zhang, J.; Zhou, Y.; Yang, L.; Wang, F.; Wang, J.; Zhou, Z.; Shen, J. Size-selected silver nanoparticles for MALDI-TOF mass spectrometry of amyloid-beta peptides. Nanoscale, 2018, 10(46), 22044-22054.
[http://dx.doi.org/10.1039/C8NR07921H ] [PMID: 30452045]
[25]
Yao, J.; Utsunomiya, S.; Kajihara, S.; Tabata, T.; Aoshima, K.; Oda, Y.; Tanaka, K. Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry. Mass Spectrom. (Tokyo), 2014, 3(1), A0030-A0030.
[http://dx.doi.org/10.5702/massspectrometry.A0030 ] [PMID: 26819872]
[26]
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, 282574-282574.
[http://dx.doi.org/10.1155/2012/282574 ] [PMID: 22611397]
[27]
Pitt, J.J. Principles and applications of liquid chromatography-mass spectrometry in clinical biochemistry. Clin. Biochem. Rev., 2009, 30(1), 19-34. [PMID: 19224008
[28]
Cobice, D.F.; Goodwin, R.J.; Andren, P.E.; Nilsson, A.; Mackay, C.L.; Andrew, R. Future technology insight: mass spectrometry imaging as a tool in drug research and development. Br. J. Pharmacol., 2015, 172(13), 3266-3283.
[http://dx.doi.org/10.1111/bph.13135 ] [PMID: 25766375]
[29]
Duncan, M.W.; Nedelkov, D.; Walsh, R.; Hattan, S.J. Applications of MALDI Mass Spectrometry in Clinical Chemistry. Clin. Chem., 2016, 62(1), 134-143.
[http://dx.doi.org/10.1373/clinchem.2015.239491 ] [PMID: 26585930]
[30]
Sokolowska, I.; Ngounou Wetie, A.G.; Woods, A.G.; Darie, C.C. Automatic determination of disulfide bridges in proteins. J. Lab. Autom., 2012, 17(6), 408-416.
[http://dx.doi.org/10.1177/2211068212454737 ] [PMID: 22885790]
[31]
Roy, U.; Woods, A.G.; Sokolowska, I.; Darie, C.C. Utility of computational structural biology in mass spectrometry. Adv. Exp. Med. Biol., 2014, 806, 107-128.
[http://dx.doi.org/10.1007/978-3-319-06068-2_6 ] [PMID: 24952181]
[32]
Jayathirtha, M.; Whitham, D.; Stradtman, S.; Darie, C.C. Recent Applications of Mass Spectrometry at Clarkson University. Adv. Exp. Med. Biol., 2019, 1140, 771-785.
[http://dx.doi.org/10.1007/978-3-030-15950-4_46 ] [PMID: 31347084]
[33]
Aslebagh, R.; Pfeffer, B.A.; Fliesler, S.J.; Darie, C.C. Mass spectrometry-based proteomics of oxidative stress: Identification of 4-hydroxy-2-nonenal (HNE) adducts of amino acids using lysozyme and bovine serum albumin as model proteins. Electrophoresis, 2016, 37(20), 2615-2623.
[http://dx.doi.org/10.1002/elps.201600134 ] [PMID: 27184861]
[34]
Signor, L.; Boeri Erba, E. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa. J. Vis. Exp., 2013, (79), 50635.
[http://dx.doi.org/10.3791/50635 ] [PMID: 24056304]
[35]
Hale, O.J.; Cooper, H.J. In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates. Biochem. Soc. Trans., 2020, 48(1), 317-326.
[http://dx.doi.org/10.1042/BST20190793 ] [PMID: 32010951]
[36]
Donnelly, D.P.; Rawlins, C.M.; DeHart, C.J.; Fornelli, L.; Schachner, L.F.; Lin, Z.; Lippens, J.L.; Aluri, K.C.; Sarin, R.; Chen, B.; Lantz, C.; Jung, W.; Johnson, K.R.; Koller, A.; Wolff, J.J.; Campuzano, I.D.G.; Auclair, J.R.; Ivanov, A.R.; Whitelegge, J.P.; Paša-Tolić, L.; Chamot-Rooke, J.; Danis, P.O.; Smith, L.M.; Tsybin, Y.O.; Loo, J.A.; Ge, Y.; Kelleher, N.L.; Agar, J.N. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nat. Methods, 2019, 16(7), 587-594.
[http://dx.doi.org/10.1038/s41592-019-0457-0 ] [PMID: 31249407]
[37]
Tipton, J.D.; Tran, J.C.; Catherman, A.D.; Ahlf, D.R.; Durbin, K.R.; Kelleher, N.L. Analysis of intact protein isoforms by mass spectrometry. J. Biol. Chem., 2011, 286(29), 25451-25458.
[http://dx.doi.org/10.1074/jbc.R111.239442 ] [PMID: 21632550]
[38]
Teramoto, K.; Sato, H.; Sun, L.; Torimura, M.; Tao, H. A simple intact protein analysis by MALDI-MS for characterization of ribosomal proteins of two genome-sequenced lactic acid bacteria and verification of their amino acid sequences. J. Proteome Res., 2007, 6(10), 3899-3907.
[http://dx.doi.org/10.1021/pr070218l ] [PMID: 17854216]
[39]
Wang, S-S. Using MALDI-TOF MS coupled with a high-mass detector to directly analyze intact proteins in thyroid tissues. Sci. China Chem., 2018, 61(7), 871-878.
[http://dx.doi.org/10.1007/s11426-017-9230-1]
[40]
Jagannadham, M.V.; Nagaraj, R. Detecting the site of phosphorylation in phosphopeptides without loss of phosphate group using MALDI TOF mass spectrometry. Anal. Chem. Insights, 2008, 3, 21-29.
[http://dx.doi.org/10.4137/ACI.S497 ] [PMID: 19609387]
[41]
Banazadeh, A.; Veillon, L.; Wooding, K.M.; Zabet-Moghaddam, M.; Mechref, Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis, 2017, 38(1), 162-189.
[http://dx.doi.org/10.1002/elps.201600357 ] [PMID: 27757981]
[42]
Wang, Y.; Liu, T.; Wu, C.; Li, H. A strategy for direct identification of protein S-nitrosylation sites by quadrupole time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom., 2008, 19(9), 1353-1360.
[http://dx.doi.org/10.1016/j.jasms.2008.06.001 ] [PMID: 18635375]
[43]
Lamotte, O.; Bertoldo, J.B.; Besson-Bard, A.; Rosnoblet, C.; Aimé, S.; Hichami, S.; Terenzi, H.; Wendehenne, D. Protein S-nitrosylation: specificity and identification strategies in plants. Front Chem., 2015, 2, 114-114.
[http://dx.doi.org/10.3389/fchem.2014.00114 ] [PMID: 25750911]
[44]
Osula, O.; Swatkoski, S.; Cotter, R.J. Identification of protein SUMOylation sites by mass spectrometry using combined microwave-assisted aspartic acid cleavage and tryptic digestion. J. Mass Spectrom., 2012, 47(5), 644-654.
[http://dx.doi.org/10.1002/jms.2959 ] [PMID: 22576878]
[45]
Xu, G.; Jaffrey, S.R. Proteomic identification of protein ubiquitination events. Biotechnol. Genet. Eng. Rev., 2013, 29(1), 73-109.
[http://dx.doi.org/10.1080/02648725.2013.801232 ] [PMID: 24568254]
[46]
Gstöttner, C.; Reusch, D.; Haberger, M.; Dragan, I.; Van Veelen, P.; Kilgour, D.P.A.; Tsybin, Y.O.; van der Burgt, Y.E.M.; Wuhrer, M.; Nicolardi, S. Monitoring glycation levels of a bispecific monoclonal antibody at subunit level by ultrahigh-resolution MALDI FT-ICR mass spectrometry. MAbs, 2020, 12(1)1682403
[http://dx.doi.org/10.1080/19420862.2019.1682403 ] [PMID: 31630606]
[47]
D’Aronco, S.; Crotti, S.; Agostini, M.; Traldi, P.; Chilelli, N.C.; Lapolla, A. The role of mass spectrometry in studies of glycation processes and diabetes management. Mass Spectrom. Rev., 2019, 38(1), 112-146.
[http://dx.doi.org/10.1002/mas.21576 ] [PMID: 30423209]
[48]
Henze, A.; Homann, T.; Rohn, I.; Aschner, M.; Link, C.D.; Kleuser, B.; Schweigert, F.J.; Schwerdtle, T.; Bornhorst, J. Caenorhabditis elegans as a model system to study post-translational modifications of human transthyretin. Sci. Rep., 2016, 6(1), 37346.
[http://dx.doi.org/10.1038/srep37346 ] [PMID: 27869126]
[49]
Soufi, Y.; Soufi, B. Mass Spectrometry-Based Bacterial Proteomics: Focus on Dermatologic Microbial Pathogens. Front. Microbiol., 2016, 7, 181.
[http://dx.doi.org/10.3389/fmicb.2016.00181 ] [PMID: 26925048]
[50]
Verrastro, I.; Pasha, S.; Jensen, K.T.; Pitt, A.R.; Spickett, C.M. Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules, 2015, 5(2), 378-411.
[http://dx.doi.org/10.3390/biom5020378 ] [PMID: 25874603]
[51]
Jiao, J.; Miao, A.; Zhang, Y.; Fan, Q.; Lu, Y.; Lu, H. Imaging phosphorylated peptide distribution in human lens by MALDI MS. Analyst (Lond.), 2015, 140(12), 4284-4290.
[http://dx.doi.org/10.1039/C5AN00101C ] [PMID: 25943257]
[52]
Pabst, M.; Küster, S.K.; Wahl, F.; Krismer, J.; Dittrich, P.S.; Zenobi, R. A Microarray-Matrix-assisted Laser Desorption/Ionization-Mass Spectrometry Approach for Site-specific Protein N-glycosylation Analysis, as Demonstrated for Human Serum Immunoglobulin M (IgM). Mol. Cell. Proteomics, 2015, 14(6), 1645-1656.
[http://dx.doi.org/10.1074/mcp.O114.046748 ] [PMID: 25802287]
[53]
Harvey, D.J. Mass spectrometric analysis of glycosylated viral proteins. Expert Rev. Proteomics, 2018, 15(5), 391-412.
[http://dx.doi.org/10.1080/14789450.2018.1468756 ] [PMID: 29707974]
[54]
Richardson, S.L.; Hanjra, P.; Zhang, G.; Mackie, B.D.; Peterson, D.L.; Huang, R. A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases. Anal. Biochem., 2015, 478, 59-64.
[http://dx.doi.org/10.1016/j.ab.2015.03.007 ] [PMID: 25778392]
[55]
Su, X.; Ren, C.; Freitas, M.A. Mass spectrometry-based strategies for characterization of histones and their post-translational modifications. Expert Rev. Proteomics, 2007, 4(2), 211-225.
[http://dx.doi.org/10.1586/14789450.4.2.211 ] [PMID: 17425457]
[56]
Noberini, R.; Sigismondo, G.; Bonaldi, T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics, 2016, 8(3), 429-445.
[http://dx.doi.org/10.2217/epi.15.108 ] [PMID: 26606673]
[57]
Garza, K.Y.; Feider, C.L.; Klein, D.R.; Rosenberg, J.A.; Brodbelt, J.S.; Eberlin, L.S. Desorption Electrospray Ionization Mass Spectrometry Imaging of Proteins Directly from Biological Tissue Sections. Anal. Chem., 2018, 90(13), 7785-7789.
[http://dx.doi.org/10.1021/acs.analchem.8b00967 ] [PMID: 29800516]
[58]
Neagu, A-N. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. Adv. Exp. Med. Biol., 2019, •••, 55-98.
[http://dx.doi.org/10.1007/978-3-030-15950-4_4]]
[59]
Caprioli, R.M.; Farmer, T.B.; Gile, J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem., 1997, 69(23), 4751-4760.
[http://dx.doi.org/10.1021/ac970888i ] [PMID: 9406525]
[60]
Chughtai, K.; Heeren, R.M.A. Mass spectrometric imaging for biomedical tissue analysis. Chem. Rev., 2010, 110(5), 3237-3277.
[http://dx.doi.org/10.1021/cr100012c ] [PMID: 20423155]
[61]
Taverna, D.; Boraldi, F.; De Santis, G.; Caprioli, R.M.; Quaglino, D. Histology-directed and imaging mass spectrometry: An emerging technology in ectopic calcification. Bone, 2015, 74, 83-94.
[http://dx.doi.org/10.1016/j.bone.2015.01.004 ] [PMID: 25595835]
[62]
Arentz, G. , 2017.
[63]
Seeley, E.H.; Caprioli, R.M. 3D imaging by mass spectrometry: a new frontier. Anal. Chem., 2012, 84(5), 2105-2110.
[http://dx.doi.org/10.1021/ac2032707 ] [PMID: 22276611]
[64]
Mourino-Alvarez, L.; Iloro, I.; de la Cuesta, F.; Azkargorta, M.; Sastre-Oliva, T.; Escobes, I.; Lopez-Almodovar, L.F.; Sanchez, P.L.; Urreta, H.; Fernandez-Aviles, F.; Pinto, A.; Padial, L.R.; Akerström, F.; Elortza, F.; Barderas, M.G. MALDI-Imaging Mass Spectrometry: a step forward in the anatomopathological characterization of stenotic aortic valve tissue. Sci. Rep., 2016, 6, 27106-27106.
[http://dx.doi.org/10.1038/srep27106 ] [PMID: 27256770]
[65]
Wisztorski, M.; Croix, D.; Macagno, E.; Fournier, I.; Salzet, M. Molecular MALDI imaging: an emerging technology for neuroscience studies. Dev. Neurobiol., 2008, 68(6), 845-858.
[http://dx.doi.org/10.1002/dneu.20623 ] [PMID: 18383549]
[66]
Grassl, J.; Taylor, N.L.; Millar, A.H. Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging. Plant Methods, 2011, 7(1), 21.
[http://dx.doi.org/10.1186/1746-4811-7-21 ] [PMID: 21726462]
[67]
Angel, P.M.; Baldwin, H.S.; Gottlieb Sen, D.; Su, Y.R.; Mayer, J.E.; Bichell, D.; Drake, R.R. Advances in MALDI imaging mass spectrometry of proteins in cardiac tissue, including the heart valve. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 927-935.
[http://dx.doi.org/10.1016/j.bbapap.2017.03.009 ] [PMID: 28341601]
[68]
Gessel, M.M.; Norris, J.L.; Caprioli, R.M. MALDI imaging mass spectrometry: spatial molecular analysis to enable a new age of discovery. J. Proteomics, 2014, 107, 71-82.
[http://dx.doi.org/10.1016/j.jprot.2014.03.021 ] [PMID: 24686089]
[69]
Dilillo, M.; Pellegrini, D.; Ait-Belkacem, R.; de Graaf, E.L.; Caleo, M.; McDonnell, L.A. Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section. J. Proteome Res., 2017, 16(8), 2993-3001.
[http://dx.doi.org/10.1021/acs.jproteome.7b00284 ] [PMID: 28648079]
[70]
Enthaler, B.; Trusch, M.; Fischer, M.; Rapp, C.; Pruns, J.K.; Vietzke, J.P. MALDI imaging in human skin tissue sections: focus on various matrices and enzymes. Anal. Bioanal. Chem., 2013, 405(4), 1159-1170.
[http://dx.doi.org/10.1007/s00216-012-6508-3 ] [PMID: 23138471]
[71]
Dilillo, M.; Ait-Belkacem, R.; Esteve, C.; Pellegrini, D.; Nicolardi, S.; Costa, M.; Vannini, E.; Graaf, E.L.; Caleo, M.; McDonnell, L.A. Ultra-High Mass Resolution MALDI Imaging Mass Spectrometry of Proteins and Metabolites in a Mouse Model of Glioblastoma. Sci. Rep., 2017, 7(1), 603.
[http://dx.doi.org/10.1038/s41598-017-00703-w ] [PMID: 28377615]
[72]
Li, Y.; Shan, M.; Zhu, Z.; Mao, X.; Yan, M.; Chen, Y.; Zhu, Q.; Li, H.; Gu, B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect. Dis., 2019, 19(1), 941.
[http://dx.doi.org/10.1186/s12879-019-4584-0 ] [PMID: 31699042]
[73]
Hou, T-Y.; Chiang-Ni, C.; Teng, S-H. Current status of MALDI-TOF mass spectrometry in clinical microbiology. Yao Wu Shi Pin Fen Xi, 2019, 27(2), 404-414.
[http://dx.doi.org/10.1016/j.jfda.2019.01.001 ] [PMID: 30987712]
[74]
Ziino, G. Reliability Evaluation of MALDI-TOF MS Associated with SARAMIS Software in Rapid Identification of Thermophilic Campylobacter Isolated from Food. Food Anal. Methods, 2019, 12(5), 1128-1132.
[http://dx.doi.org/10.1007/s12161-019-01447-1]
[75]
Patel, R. MALDI-TOF MS for the diagnosis of infectious diseases. Clin. Chem., 2015, 61(1), 100-111.
[http://dx.doi.org/10.1373/clinchem.2014.221770 ] [PMID: 25278500]
[76]
Flores-Treviño, S.; Garza-González, E.; Mendoza-Olazarán, S.; Morfín-Otero, R.; Camacho-Ortiz, A.; Rodríguez-Noriega, E.; Martínez-Meléndez, A.; Bocanegra-Ibarias, P. Screening of biomarkers of drug resistance or virulence in ESCAPE pathogens by MALDI-TOF mass spectrometry. Sci. Rep., 2019, 9(1), 18945.
[http://dx.doi.org/10.1038/s41598-019-55430-1 ] [PMID: 31831867]
[77]
Vrioni, G.; Tsiamis, C.; Oikonomidis, G.; Theodoridou, K.; Kapsimali, V.; Tsakris, A. MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives. Ann. Transl. Med., 2018, 6(12), 240-240.
[http://dx.doi.org/10.21037/atm.2018.06.28 ] [PMID: 30069442]
[78]
Cobo, F. Application of maldi-tof mass spectrometry in clinical virology: a review. Open Virol. J., 2013, 7, 84-90.
[http://dx.doi.org/10.2174/1874357920130927003 ] [PMID: 24222805]
[79]
Calderaro, A.; Arcangeletti, M.C.; Rodighiero, I.; Buttrini, M.; Montecchini, S.; Vasile Simone, R.; Medici, M.C.; Chezzi, C.; De Conto, F. Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Sci. Rep., 2016, 6(1), 36082.
[http://dx.doi.org/10.1038/srep36082 ] [PMID: 27786297]
[80]
Liu, N.; Wang, L.; Cai, G.; Zhang, D.; Lin, J. Establishment of a simultaneous detection method for ten duck viruses using MALDI-TOF mass spectrometry. J. Virol. Methods, 2019, •••273113723
[http://dx.doi.org/10.1016/j.jviromet.2019.113723 ] [PMID: 31430495]
[81]
Xiu, L.; Zhang, C.; Wu, Z.; Peng, J. Establishment and Application of a Universal Coronavirus Screening Method Using MALDI-TOF Mass Spectrometry. Front. Microbiol., 2017, 8, 1510-1510.
[http://dx.doi.org/10.3389/fmicb.2017.01510 ] [PMID: 28848521]
[82]
Nakamura, S.; Sato, H.; Tanaka, R.; Yaguchi, T. Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification. Mass Spectrom. (Tokyo), 2016, 5(1), A0049-A0049.
[http://dx.doi.org/10.5702/massspectrometry.A0049 ] [PMID: 27843740]
[83]
Patel, R. A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification. J. Fungi (Basel), 2019, 5(1), 4.
[http://dx.doi.org/10.3390/jof5010004 ] [PMID: 30609833]
[84]
Ziegler, D.; Pothier, J.F.; Ardley, J.; Fossou, R.K.; Pflüger, V.; de Meyer, S.; Vogel, G.; Tonolla, M.; Howieson, J.; Reeve, W.; Perret, X. Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS. Appl. Microbiol. Biotechnol., 2015, 99(13), 5547-5562.
[http://dx.doi.org/10.1007/s00253-015-6515-3 ] [PMID: 25776061]
[85]
Dunham, S.J.B.; Ellis, J.F.; Li, B.; Sweedler, J.V. Mass Spectrometry Imaging of Complex Microbial Communities. Acc. Chem. Res., 2017, 50(1), 96-104.
[http://dx.doi.org/10.1021/acs.accounts.6b00503 ] [PMID: 28001363]
[86]
Santos, T.; Théron, L.; Chambon, C.; Viala, D.; Centeno, D.; Esbelin, J.; Hébraud, M. MALDI mass spectrometry imaging and in situ microproteomics of Listeria monocytogenes biofilms. J. Proteomics, 2018, 187, 152-160.
[http://dx.doi.org/10.1016/j.jprot.2018.07.012 ] [PMID: 30071319]
[87]
Rodríguez-Sánchez, B. Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018.
[88]
Sambou, M.; Aubadie-Ladrix, M.; Fenollar, F.; Fall, B.; Bassene, H.; Almeras, L.; Sambe-Ba, B.; Perrot, N.; Chatellier, S.; Faye, N.; Parola, P.; Wade, B.; Raoult, D.; Mediannikov, O. Comparison of matrix-assisted laser desorption ionization-time of flight mass spectrometry and molecular biology techniques for identification of Culicoides (Diptera: ceratopogonidae) biting midges in senegal. J. Clin. Microbiol., 2015, 53(2), 410-418.
[http://dx.doi.org/10.1128/JCM.01855-14 ] [PMID: 25411169]
[89]
Boyer, P.H.; Almeras, L.; Plantard, O.; Grillon, A.; Talagrand-Reboul, É.; McCoy, K.; Jaulhac, B.; Boulanger, N. Identification of closely related Ixodes species by protein profiling with MALDI-TOF mass spectrometry. PLoS One, 2019, 14(10), e0223735-e0223735.
[http://dx.doi.org/10.1371/journal.pone.0223735 ] [PMID: 31622384]
[90]
Feucherolles, M.; Poppert, S.; Utzinger, J.; Becker, S.L. MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review. Parasit. Vectors, 2019, 12(1), 245-245.
[http://dx.doi.org/10.1186/s13071-019-3493-9 ] [PMID: 31101120]
[91]
Jaegger, C.F.; Negrão, F.; Assis, D.M.; Belaz, K.R.A.; Angolini, C.F.F.; Fernandes, A.M.A.P.; Santos, V.G.; Pimentel, A.; Abánades, D.R.; Giorgio, S.; Eberlin, M.N.; Rocha, D.F.O. MALDI MS imaging investigation of the host response to visceral leishmaniasis. Mol. Biosyst., 2017, 13(10), 1946-1953.
[http://dx.doi.org/10.1039/C7MB00306D ] [PMID: 28758666]
[92]
Negrão, F. de O Rocha, D.F.; Jaeeger, C.F.; Rocha, F.J.S.; Eberlin, M.N.; Giorgio, S. Murine cutaneous leishmaniasis investigated by MALDI mass spectrometry imaging. Mol. Biosyst., 2017, 13(10), 2036-2043.
[http://dx.doi.org/10.1039/C7MB00411G ] [PMID: 28783195]
[93]
Tandina, F.; Laroche, M.; Davoust, B.K.; Doumbo, O.; Parola, P. Blood meal identification in the cryptic species Anopheles gambiae and Anopheles coluzzii using MALDI-TOF MS. Parasite, 2018, 25, 40-40.
[http://dx.doi.org/10.1051/parasite/2018041 ] [PMID: 30052501]
[94]
Niare, S.; Almeras, L.; Tandina, F.; Yssouf, A.; Bacar, A.; Toilibou, A.; Doumbo, O.; Raoult, D.; Parola, P. MALDI-TOF MS identification of Anopheles gambiae Giles blood meal crushed on Whatman filter papers. PLoS One, 2017, 12(8), e0183238-e0183238.
[http://dx.doi.org/10.1371/journal.pone.0183238 ] [PMID: 28817629]
[95]
Dowd, S.E.; Mustroph, M.L.; Romanova, E.V.; Southey, B.R.; Pinardo, H.; Rhodes, J.S.; Sweedler, J.V. Exploring Exercise- and Context-Induced Peptide Changes in Mice by Quantitative Mass Spectrometry. ACS Omega, 2018, 3(10), 13817-13827.
[http://dx.doi.org/10.1021/acsomega.8b01713 ] [PMID: 30411050]
[96]
Jiang, Y.; Sun, J.; Huang, X.; Shi, H.; Xiong, C.; Nie, Z. Direct identification of forensic body fluids by MALDI-MS. Analyst (Lond.), 2019, 144(23), 7017-7023.
[http://dx.doi.org/10.1039/C9AN01385G ] [PMID: 31647064]
[97]
Fredriksson, S-A.; Hulst, A.G.; Artursson, E.; de Jong, A.L.; Nilsson, C.; van Baar, B.L. Forensic identification of neat ricin and of ricin from crude castor bean extracts by mass spectrometry. Anal. Chem., 2005, 77(6), 1545-1555.
[http://dx.doi.org/10.1021/ac048756u ] [PMID: 15762556]
[98]
Alam, S.I.; Kumar, B.; Kamboj, D.V. Multiplex detection of protein toxins using MALDI-TOF-TOF tandem mass spectrometry: application in unambiguous toxin detection from bioaerosol. Anal. Chem., 2012, 84(23), 10500-10507.
[http://dx.doi.org/10.1021/ac3028678 ] [PMID: 23083074]
[99]
Pieri, M.; Lombardi, A.; Basilicata, P.; Mamone, G.; Picariello, G. Proteomics in Forensic Sciences: Identification of the Nature of the Last Meal at Autopsy. J. Proteome Res., 2018, 17(7), 2412-2420.
[http://dx.doi.org/10.1021/acs.jproteome.8b00159 ] [PMID: 29851351]
[100]
Procopio, N.; Williams, A.; Chamberlain, A.T.; Buckley, M. Forensic proteomics for the evaluation of the post-mortem decay in bones. J. Proteomics, 2018, 177, 21-30.
[http://dx.doi.org/10.1016/j.jprot.2018.01.016 ] [PMID: 29407476]
[101]
Parker, G.J.; Leppert, T.; Anex, D.S.; Hilmer, J.K.; Matsunami, N.; Baird, L.; Stevens, J.; Parsawar, K.; Durbin-Johnson, B.P.; Rocke, D.M.; Nelson, C.; Fairbanks, D.J.; Wilson, A.S.; Rice, R.H.; Woodward, S.R.; Bothner, B.; Hart, B.R.; Leppert, M. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLoS One, 2016, 11(9), e0160653-e0160653.
[http://dx.doi.org/10.1371/journal.pone.0160653 ] [PMID: 27603779]
[102]
Duriez, E.; Armengaud, J.; Fenaille, F.; Ezan, E. Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications. J. Mass Spectrom., 2016, 51(3), 183-199.
[http://dx.doi.org/10.1002/jms.3747 ] [PMID: 26956386]
[103]
Tevell Åberg, A.; Björnstad, K.; Hedeland, M. Mass spectrometric detection of protein-based toxins. Biosecur. Bioterror., 2013, 11(S1)(Suppl. 1), S215-S226.
[http://dx.doi.org/10.1089/bsp.2012.0072 ] [PMID: 23971809]
[104]
Mertz, L.; New Forensics Methods Looking More Like, C.S.I. New Forensics Methods Looking More Like CSI: Rapid DNA Analysis, Proteomics, and New Technology Increasingly Impact Forensics Investigations. IEEE Pulse, 2017, 8(6), 40-45.
[http://dx.doi.org/10.1109/MPUL.2017.2750838 ] [PMID: 29155377]
[105]
Deininger, L.; Patel, E.; Clench, M.R.; Sears, V.; Sammon, C.; Francese, S. Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks. Proteomics, 2016, 16(11-12), 1707-1717.
[http://dx.doi.org/10.1002/pmic.201500544 ] [PMID: 27125769]
[106]
Bradshaw, R.; Denison, N.; Francese, S. Implementation of MALDI MS profiling and imaging methods for the analysis of real crime scene fingermarks. Analyst (Lond.), 2017, 142(9), 1581-1590.
[http://dx.doi.org/10.1039/C7AN00218A ] [PMID: 28387396]
[107]
Li, C.; Li, Z.; Tuo, Y.; Ma, D.; Shi, Y.; Zhang, Q.; Zhuo, X.; Deng, K.; Chen, Y.; Wang, Z.; Huang, P. MALDI-TOF MS as a Novel Tool for the Estimation of Postmortem Interval in Liver Tissue Samples. Sci. Rep., 2017, 7(1), 4887.
[http://dx.doi.org/10.1038/s41598-017-05216-0 ] [PMID: 28687792]
[108]
Poetzsch, M.; Steuer, A.E.; Roemmelt, A.T.; Baumgartner, M.R.; Kraemer, T. Single hair analysis of small molecules using MALDI-triple quadrupole MS imaging and LC-MS/MS: investigations on opportunities and pitfalls. Anal. Chem., 2014, 86(23), 11758-11765.
[http://dx.doi.org/10.1021/ac503193w ] [PMID: 25289728]
[109]
Portevin, D.; Pflüger, V.; Otieno, P.; Brunisholz, R.; Vogel, G.; Daubenberger, C. Quantitative whole-cell MALDI-TOF MS fingerprints distinguishes human monocyte sub-populations activated by distinct microbial ligands. BMC Biotechnol., 2015, 15(1), 24.
[http://dx.doi.org/10.1186/s12896-015-0140-1 ] [PMID: 25887592]
[110]
Holzlechner, M.; Strasser, K.; Zareva, E.; Steinhäuser, L.; Birnleitner, H.; Beer, A.; Bergmann, M.; Oehler, R.; Marchetti-Deschmann, M. In Situ Characterization of Tissue-Resident Immune Cells by MALDI Mass Spectrometry Imaging. J. Proteome Res., 2017, 16(1), 65-76.
[http://dx.doi.org/10.1021/acs.jproteome.6b00610 ] [PMID: 27755872]
[111]
Francese, S.; Lambardi, D.; Mastrobuoni, G.; la Marca, G.; Moneti, G.; Turillazzi, S. Detection of honeybee venom in envenomed tissues by direct MALDI MSI. J. Am. Soc. Mass Spectrom., 2009, 20(1), 112-123.
[http://dx.doi.org/10.1016/j.jasms.2008.09.006 ] [PMID: 18849171]
[112]
Stahl, A.; Schröder, U. Development of a MALDI-TOF MS-Based Protein Fingerprint Database of Common Food Fish Allowing Fast and Reliable Identification of Fraud and Substitution. J. Agric. Food Chem., 2017, 65(34), 7519-7527.
[http://dx.doi.org/10.1021/acs.jafc.7b02826 ] [PMID: 28745053]
[113]
Di Francesco, L.; Di Girolamo, F.; Mennini, M.; Masotti, A.; Salvatori, G.; Rigon, G.; Signore, F.; Pietrantoni, E.; Scapaticci, M.; Lante, I.; Goffredo, B.M.; Mazzina, O.; Elbousify, A.I.; Roncada, P.; Dotta, A.; Fiocchi, A.; Putignani, L. A MALDI-TOF MS approach for mammalian, human, and formula milks’ profiling. Nutrients, 2018, 10(9), 1238.
[http://dx.doi.org/10.3390/nu10091238 ] [PMID: 30189627]
[114]
Hynek, R.; Kuckova, S.; Hradilova, J.; Kodicek, M. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry as a tool for fast identification of protein binders in color layers of paintings. Rapid Commun. Mass Spectrom., 2004, 18(17), 1896-1900.
[http://dx.doi.org/10.1002/rcm.1570 ] [PMID: 15329854]
[115]
Woods, A. , 2013.
[116]
Suarez, N.; Morais, V. Identification of Venom-Specific Fingerprints of Clinically Relevant Uruguayan Snakes by MALDI-TOF. Am. J. Biochem. Biotechnol., 2019, 15, 119-124.
[http://dx.doi.org/10.3844/ajbbsp.2019.119.124]
[117]
Matysiak, J. Proteomic analysis of Apis mellifera venom determined by liquid chromatography (LC) coupled with nano-LC-MALDI-TOF/TOF MS. Acta Poloniae Pharmaceutica -. Drug Res. (Stuttg.), 2017, 74, 53-65. [PMID: 29474761
[118]
Guráň, R. MALDI-TOF MSI and electrochemical detection of metallothionein in chicken liver after cadmium exposure. J. Metallomi. Nanotech., 2015, 2(3), 43-49.
[119]
Lagarrigue, M.; Caprioli, R.M.; Pineau, C. Potential of MALDI imaging for the toxicological evaluation of environmental pollutants. J. Proteomics, 2016, 144, 133-139.
[http://dx.doi.org/10.1016/j.jprot.2016.05.008 ] [PMID: 27178109]
[120]
Zhang, X.; Yuan, Z.; Shen, B.; Zhu, M.; Liu, C.; Xu, W. Discovery of serum protein biomarkers in rheumatoid arthritis using MALDI-TOF-MS combined with magnetic beads. Clin. Exp. Med., 2012, 12(3), 145-151.
[http://dx.doi.org/10.1007/s10238-011-0154-5 ] [PMID: 21922190]
[121]
Gao, J.; Meyer, K.; Borucki, K.; Ueland, P.M. Multiplex Immuno-MALDI-TOF MS for Targeted Quantification of Protein Biomarkers and Their Proteoforms Related to Inflammation and Renal Dysfunction. Anal. Chem., 2018, 90(5), 3366-3373.
[http://dx.doi.org/10.1021/acs.analchem.7b04975 ] [PMID: 29420882]
[122]
Conraux, L.; Pech, C.; Guerraoui, H.; Loyaux, D.; Ferrara, P.; Guillemot, J.C.; Meininger, V.; Pradat, P.F.; Salachas, F.; Bruneteau, G.; Le Forestier, N.; Lacomblez, L. Plasma peptide biomarker discovery for amyotrophic lateral sclerosis by MALDI-TOF mass spectrometry profiling. PLoS One, 2013, 8(11), e79733-e79733.
[http://dx.doi.org/10.1371/journal.pone.0079733 ] [PMID: 24224000]
[123]
Swiatly, A.; Horala, A.; Hajduk, J.; Matysiak, J.; Nowak-Markwitz, E.; Kokot, Z.J. MALDI-TOF-MS analysis in discovery and identification of serum proteomic patterns of ovarian cancer. BMC Cancer, 2017, 17(1), 472.
[http://dx.doi.org/10.1186/s12885-017-3467-2 ] [PMID: 28683725]
[124]
Rodrigo, M.A.; Zitka, O.; Krizkova, S.; Moulick, A.; Adam, V.; Kizek, R. MALDI-TOF MS as evolving cancer diagnostic tool: a review. J. Pharm. Biomed. Anal., 2014, 95, 245-255.
[http://dx.doi.org/10.1016/j.jpba.2014.03.007 ] [PMID: 24699369]
[125]
Hortin, G.L. The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin. Chem., 2006, 52(7), 1223-1237.
[http://dx.doi.org/10.1373/clinchem.2006.069252 ] [PMID: 16644871]
[126]
Nedelkov, D.; Nelson, R.W. Analysis of human urine protein biomarkers via biomolecular interaction analysis mass spectrometry. Am. J. Kidney Dis., 2001, 38(3), 481-487.
[http://dx.doi.org/10.1053/ajkd.2001.26831 ] [PMID: 11532678]
[127]
Bharucha, T.; Gangadharan, B.; Kumar, A.; de Lamballerie, X.; Newton, P.N.; Winterberg, M.; Dubot-Pérès, A.; Zitzmann, N. Mass spectrometry-based proteomic techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections. A systematic review. J. Infect., 2019, 79(5), 407-418.
[http://dx.doi.org/10.1016/j.jinf.2019.08.005 ] [PMID: 31404562]
[128]
Ploypetch, S.; Roytrakul, S.; Jaresitthikunchai, J.; Phaonakrop, N.; Krobthong, S.; Suriyaphol, G. Salivary proteomics of canine oral tumors using MALDI-TOF mass spectrometry and LC-tandem mass spectrometry. PLoS One, 2019, 14(7), e0219390-e0219390.
[http://dx.doi.org/10.1371/journal.pone.0219390 ] [PMID: 31318878]
[129]
Prodan, A.; Brand, H.; Imangaliyev, S.; Tsivtsivadze, E.; van der Weijden, F.; de Jong, A.; Paauw, A.; Crielaard, W.; Keijser, B.; Veerman, E. A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS. PLoS One, 2016, 11(6), e0156707-e0156707.
[http://dx.doi.org/10.1371/journal.pone.0156707 ] [PMID: 27258023]
[130]
Sun, X.; Huang, X.; Tan, X.; Si, Y.; Wang, X.; Chen, F.; Zheng, S. Salivary peptidome profiling for diagnosis of severe early childhood caries. J. Transl. Med., 2016, 14(1), 240.
[http://dx.doi.org/10.1186/s12967-016-0996-4 ] [PMID: 27527350]
[131]
Šebela, M.; Jahodářová, E.; Raus, M.; Lenobel, R.; Hašler, P. Intact cell MALDI-TOF mass spectrometric analysis of Chroococcidiopsis cyanobacteria for classification purposes and identification of possible marker proteins. PLoS One, 2018, 13(11), e0208275-e0208275.
[http://dx.doi.org/10.1371/journal.pone.0208275 ] [PMID: 30496311]
[132]
Shariatgorji, M.; Nilsson, A.; Fridjonsdottir, E.; Vallianatou, T.; Källback, P.; Katan, L.; Sävmarker, J.; Mantas, I.; Zhang, X.; Bezard, E.; Svenningsson, P.; Odell, L.R.; Andrén, P.E. Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging. Nat. Methods, 2019, 16(10), 1021-1028.
[http://dx.doi.org/10.1038/s41592-019-0551-3 ] [PMID: 31548706]
[133]
Shariatgorji, M.; Svenningsson, P.; Andrén, P.E. Mass spectrometry imaging, an emerging technology in neuropsychopharmacology. Neuropsychopharmacology, 2014, 39(1), 34-49.
[http://dx.doi.org/10.1038/npp.2013.215 ] [PMID: 23966069]
[134]
Zimmerman, T.A.; Rubakhin, S.S.; Sweedler, J.V. MALDI mass spectrometry imaging of neuronal cell cultures. J. Am. Soc. Mass Spectrom., 2011, 22(5), 828-836.
[http://dx.doi.org/10.1007/s13361-011-0111-2 ] [PMID: 21472517]
[135]
Ong, T-H.; Romanova, E.V.; Roberts-Galbraith, R.H.; Yang, N.; Zimmerman, T.A.; Collins, J.J., III; Lee, J.E.; Kelleher, N.L.; Newmark, P.A.; Sweedler, J.V. Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea. J. Biol. Chem., 2016, 291(15), 8109-8120.
[http://dx.doi.org/10.1074/jbc.M115.709196 ] [PMID: 26884331]
[136]
Chen, R.; Ouyang, C.; Xiao, M.; Li, L. In situ identification and mapping of neuropeptides from the stomatogastric nervous system of Cancer borealis. Rapid Commun. Mass Spectrom., 2014, 28(22), 2437-2444.
[http://dx.doi.org/10.1002/rcm.7037 ] [PMID: 25303472]
[137]
Schober, Y.; Schramm, T.; Spengler, B.; Römpp, A. Protein identification by accurate mass matrix-assisted laser desorption/ionization imaging of tryptic peptides. Rapid Commun. Mass Spectrom., 2011, 25(17), 2475-2483.
[http://dx.doi.org/10.1002/rcm.5135 ] [PMID: 21818808]
[138]
Tucker, K.R.; Serebryannyy, L.A.; Zimmerman, T.A.; Rubakhin, S.S.; Sweedler, J.V. The modified-bead stretched sample method: development and application to MALDI-MS imaging of protein localization in the spinal cord. Chem. Sci. (Camb.), 2011, 2(4), 785-795.
[http://dx.doi.org/10.1039/c0sc00563k ] [PMID: 21625333]
[139]
Sui, P. , 2017.
[140]
Monroe, E.B.; Annangudi, S.P.; Hatcher, N.G.; Gutstein, H.B.; Rubakhin, S.S.; Sweedler, J.V. SIMS and MALDI MS imaging of the spinal cord. Proteomics, 2008, 8(18), 3746-3754.
[http://dx.doi.org/10.1002/pmic.200800127 ] [PMID: 18712768]
[141]
Rubakhin, S.S.; Ulanov, A.; Sweedler, J.V. Mass Spectrometry Imaging and GC-MS Profiling of the Mammalian Peripheral Sensory-Motor Circuit. J. Am. Soc. Mass Spectrom., 2015, 26(6), 958-966.
[http://dx.doi.org/10.1007/s13361-015-1128-8 ] [PMID: 25822927]
[142]
Schubert, K.O.; Weiland, F.; Baune, B.T.; Hoffmann, P. The use of MALDI-MSI in the investigation of psychiatric and neurodegenerative disorders: A review. Proteomics, 2016, 16(11-12), 1747-1758.
[http://dx.doi.org/10.1002/pmic.201500460 ] [PMID: 27303929]
[143]
Woods, A.G.; Ngounou Wetie, A.G.; Sokolowska, I.; Russell, S.; Ryan, J.P.; Michel, T.M.; Thome, J.; Darie, C.C. Mass spectrometry as a tool for studying autism spectrum disorder. J. Mol. Psychiatry, 2013, 1(1), 6-6.
[http://dx.doi.org/10.1186/2049-9256-1-6 ] [PMID: 25408899]
[144]
González de San Román, E.; Bidmon, H.J.; Malisic, M.; Susnea, I.; Küppers, A.; Hübbers, R.; Wree, A.; Nischwitz, V.; Amunts, K.; Huesgen, P.F. Molecular composition of the human primary visual cortex profiled by multimodal mass spectrometry imaging. Brain Struct. Funct., 2018, 223(6), 2767-2783.
[http://dx.doi.org/10.1007/s00429-018-1660-y ] [PMID: 29633039]
[145]
Kakuda, N.; Miyasaka, T.; Iwasaki, N.; Nirasawa, T.; Wada-Kakuda, S.; Takahashi-Fujigasaki, J.; Murayama, S.; Ihara, Y.; Ikegawa, M. Distinct deposition of amyloid-β species in brains with Alzheimer’s disease pathology visualized with MALDI imaging mass spectrometry. Acta Neuropathol. Commun., 2017, 5(1), 73.
[http://dx.doi.org/10.1186/s40478-017-0477-x ] [PMID: 29037261]
[146]
Ho Kim, J.; Franck, J.; Kang, T.; Heinsen, H.; Ravid, R.; Ferrer, I.; Hee Cheon, M.; Lee, J.Y.; Shin Yoo, J.; Steinbusch, H.W.; Salzet, M.; Fournier, I.; Mok Park, Y. Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer’s disease. Sci. Rep., 2015, 5, 11138.
[http://dx.doi.org/10.1038/srep11138 ] [PMID: 26059363]
[147]
Martin-Lorenzo, M.; Alvarez-Llamas, G.; McDonnell, L.A.; Vivanco, F. Molecular histology of arteries: mass spectrometry imaging as a novel ex vivo tool to investigate atherosclerosis. Expert Rev. Proteomics, 2016, 13(1), 69-81.
[http://dx.doi.org/10.1586/14789450.2016.1116944 ] [PMID: 26558814]
[148]
Martin-Lorenzo, M.; Balluff, B.; Maroto, A.S.; Carreira, R.J.; van Zeijl, R.J.; Gonzalez-Calero, L.; de la Cuesta, F.; Barderas, M.G.; Lopez-Almodovar, L.F.; Padial, L.R.; McDonnell, L.A.; Vivanco, F.; Alvarez-Llamas, G. Lipid and protein maps defining arterial layers in atherosclerotic aorta. Data Brief, 2015, 4, 328-331.
[http://dx.doi.org/10.1016/j.dib.2015.06.005 ] [PMID: 26217810]
[149]
Martin-Lorenzo, M.; Balluff, B.; Maroto, A.S.; Carreira, R.J.; van Zeijl, R.J.; Gonzalez-Calero, L.; de la Cuesta, F.; Barderas, M.G.; Lopez-Almodovar, L.F.; Padial, L.R.; McDonnell, L.A.; Vivanco, F.; Alvarez-Llamas, G. Molecular anatomy of ascending aorta in atherosclerosis by MS Imaging: Specific lipid and protein patterns reflect pathology. J. Proteomics, 2015, 126, 245-251.
[http://dx.doi.org/10.1016/j.jprot.2015.06.005 ] [PMID: 26079611]
[150]
Martin-Lorenzo, M.; Balluff, B.; Sanz-Maroto, A.; van Zeijl, R.J.; Vivanco, F.; Alvarez-Llamas, G.; McDonnell, L.A. 30μm spatial resolution protein MALDI MSI: In-depth comparison of five sample preparation protocols applied to human healthy and atherosclerotic arteries. J. Proteomics, 2014, 108, 465-468.
[http://dx.doi.org/10.1016/j.jprot.2014.06.013 ] [PMID: 24972319]
[151]
Noronha, A.M.; Linden, C.; Sharma, P. Developments in Cardiovascular Proteomics. J. Proteomics Bioinform., 2016, 9, 144-150.
[152]
Yajima, Y.; Hiratsuka, T.; Kakimoto, Y.; Ogawa, S.; Shima, K.; Yamazaki, Y.; Yoshikawa, K.; Tamaki, K.; Tsuruyama, T. Region of Interest analysis using mass spectrometry imaging of mitochondrial and sarcomeric proteins in acute cardiac infarction tissue. Sci. Rep., 2018, 8(1), 7493.
[http://dx.doi.org/10.1038/s41598-018-25817-7 ] [PMID: 29748547]
[153]
Lefcoski, S.; Kew, K.; Reece, S.; Torres, M.J.; Parks, J.; Reece, S.; de Castro Brás, L.E.; Virag, J.A.I. Anatomical-Molecular Distribution of EphrinA1 in Infarcted Mouse Heart Using MALDI Mass Spectrometry Imaging. J. Am. Soc. Mass Spectrom., 2018, 29(3), 527-534.
[http://dx.doi.org/10.1007/s13361-017-1869-7 ] [PMID: 29305797]
[154]
Cillero-Pastor, B.; Eijkel, G.B.; Kiss, A.; Blanco, F.J.; Heeren, R.M. Matrix-assisted laser desorption ionization-imaging mass spectrometry: a new methodology to study human osteoarthritic cartilage. Arthritis Rheum., 2013, 65(3), 710-720.
[http://dx.doi.org/10.1002/art.37799 ] [PMID: 23280504]
[155]
Rocha, B.; Cillero-Pastor, B.; Blanco, F.J.; Ruiz-Romero, C. MALDI mass spectrometry imaging in rheumatic diseases. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 784-794.
[http://dx.doi.org/10.1016/j.bbapap.2016.10.004 ] [PMID: 27742553]
[156]
Ronci, M.; Sharma, S.; Chataway, T.; Burdon, K.P.; Martin, S.; Craig, J.E.; Voelcker, N.H. MALDI-MS-imaging of whole human lens capsule. J. Proteome Res., 2011, 10(8), 3522-3529.
[http://dx.doi.org/10.1021/pr200148k ] [PMID: 21663315]
[157]
Han, J.; Schey, K.L. MALDI tissue imaging of ocular lens α-crystallin. Invest. Ophthalmol. Vis. Sci., 2006, 47(7), 2990-2996.
[http://dx.doi.org/10.1167/iovs.05-1529 ] [PMID: 16799044]
[158]
Grey, A.C.; Schey, K.L. Age-related changes in the spatial distribution of human lens alpha-crystallin products by MALDI imaging mass spectrometry. Invest. Ophthalmol. Vis. Sci., 2009, 50(9), 4319-4329.
[http://dx.doi.org/10.1167/iovs.09-3522 ] [PMID: 19387068]
[159]
Grey, A.C.; Chaurand, P.; Caprioli, R.M.; Schey, K.L. MALDI imaging mass spectrometry of integral membrane proteins from ocular lens and retinal tissue. J. Proteome Res., 2009, 8(7), 3278-3283.
[http://dx.doi.org/10.1021/pr800956y ] [PMID: 19326924]
[160]
Kriegsmann, J.; Kriegsmann, M.; Casadonte, R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics. Int. J. Oncol., 2015, 46(3), 893-906. [review]. [https://dx.doi.org/10.3892/ijo.2014.2788
[PMID: 25482502]
[161]
Le Rhun, E.; Duhamel, M.; Wisztorski, M.; Gimeno, J.P.; Zairi, F.; Escande, F.; Reyns, N.; Kobeissy, F.; Maurage, C.A.; Salzet, M.; Fournier, I. Evaluation of non-supervised MALDI mass spectrometry imaging combined with microproteomics for glioma grade III classification. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 875-890.
[http://dx.doi.org/10.1016/j.bbapap.2016.11.012 ] [PMID: 27890679]
[162]
Boskamp, T.; Lachmund, D.; Oetjen, J.; Cordero Hernandez, Y.; Trede, D.; Maass, P.; Casadonte, R.; Kriegsmann, J.; Warth, A.; Dienemann, H.; Weichert, W.; Kriegsmann, M. A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 916-926.
[http://dx.doi.org/10.1016/j.bbapap.2016.11.003 ] [PMID: 27836618]
[163]
Grüner, B.M.; Hahne, H.; Mazur, P.K.; Trajkovic-Arsic, M.; Maier, S.; Esposito, I.; Kalideris, E.; Michalski, C.W.; Kleeff, J.; Rauser, S.; Schmid, R.M.; Küster, B.; Walch, A.; Siveke, J.T. MALDI imaging mass spectrometry for in situ proteomic analysis of preneoplastic lesions in pancreatic cancer. PLoS One, 2012, 7(6), e39424-e39424.
[http://dx.doi.org/10.1371/journal.pone.0039424 ] [PMID: 22761793]
[164]
Mittal, P.; Klingler-Hoffmann, M.; Arentz, G.; Winderbaum, L.; Kaur, G.; Anderson, L.; Scurry, J.; Leung, Y.; Stewart, C., Jr; Carter, J.; Hoffmann, P.; Oehler, M.K. Annexin A2 and alpha actinin 4 expression correlates with metastatic potential of primary endometrial cancer. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 846-857.
[165]
Zhang, C.; Arentz, G.; Winderbaum, L.; Lokman, N.A.; Klingler-Hoffmann, M.; Mittal, P.; Carter, C.; Oehler, M.K.; Hoffmann, P. MALDI Mass Spectrometry Imaging Reveals Decreased CK5 Levels in Vulvar Squamous Cell Carcinomas Compared to the Precursor Lesion Differentiated Vulvar Intraepithelial Neoplasia. Int. J. Mol. Sci., 2016, 17(7), 1088.
[http://dx.doi.org/10.3390/ijms17071088 ] [PMID: 27399691]
[166]
Gustafsson, J.O.R.; Oehler, M.K.; Ruszkiewicz, A.; McColl, S.R.; Hoffmann, P. MALDI Imaging Mass Spectrometry (MALDI-IMS)-application of spatial proteomics for ovarian cancer classification and diagnosis. Int. J. Mol. Sci., 2011, 12(1), 773-794.
[http://dx.doi.org/10.3390/ijms12010773 ] [PMID: 21340013]
[167]
Toss, A.; De Matteis, E.; Rossi, E.; Casa, L.D.; Iannone, A.; Federico, M.; Cortesi, L. Ovarian cancer: can proteomics give new insights for therapy and diagnosis? Int. J. Mol. Sci., 2013, 14(4), 8271-8290.
[http://dx.doi.org/10.3390/ijms14048271 ] [PMID: 23591842]
[168]
Delcourt, V.; Franck, J.; Leblanc, E.; Narducci, F.; Robin, Y.M.; Gimeno, J.P.; Quanico, J.; Wisztorski, M.; Kobeissy, F.; Jacques, J.F.; Roucou, X.; Salzet, M.; Fournier, I. Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine, 2017, 21, 55-64.
[http://dx.doi.org/10.1016/j.ebiom.2017.06.001 ] [PMID: 28629911]
[169]
Lemaire, R.; Menguellet, S.A.; Stauber, J.; Marchaudon, V.; Lucot, J.P.; Collinet, P.; Farine, M.O.; Vinatier, D.; Day, R.; Ducoroy, P.; Salzet, M.; Fournier, I. Specific MALDI imaging and profiling for biomarker hunting and validation: fragment of the 11S proteasome activator complex, Reg alpha fragment, is a new potential ovary cancer biomarker. J. Proteome Res., 2007, 6(11), 4127-4134.
[http://dx.doi.org/10.1021/pr0702722 ] [PMID: 17939699]
[170]
Gagnon, H.; Franck, J.; Wisztorski, M.; Day, R.; Fournier, I.; Salzet, M. Targeted mass spectrometry imaging: specific targeting mass spectrometry imaging technologies from history to perspective. Prog. Histochem. Cytochem., 2012, 47(3), 133-174.
[http://dx.doi.org/10.1016/j.proghi.2012.08.002 ] [PMID: 22985794]
[171]
Rauser, S.; Marquardt, C.; Balluff, B.; Deininger, S.O.; Albers, C.; Belau, E.; Hartmer, R.; Suckau, D.; Specht, K.; Ebert, M.P.; Schmitt, M.; Aubele, M.; Höfler, H.; Walch, A. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J. Proteome Res., 2010, 9(4), 1854-1863.
[http://dx.doi.org/10.1021/pr901008d ] [PMID: 20170166]
[172]
Végvári, Á.; Shavkunov, A.S.; Fehniger, T.E.; Grabau, D.; Niméus, E.; Marko-Varga, G. Localization of tamoxifen in human breast cancer tumors by MALDI mass spectrometry imaging. Clin. Transl. Med., 2016, 5(1), 10.
[http://dx.doi.org/10.1186/s40169-016-0090-9 ] [PMID: 26965929]
[173]
Dekker, T.J.A.; Balluff, B.D.; Jones, E.A.; Schöne, C.D.; Schmitt, M.; Aubele, M.; Kroep, J.R.; Smit, V.T.; Tollenaar, R.A.; Mesker, W.E.; Walch, A.; McDonnell, L.A. Multicenter matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) identifies proteomic differences in breast-cancer-associated stroma. J. Proteome Res., 2014, 13(11), 4730-4738.
[http://dx.doi.org/10.1021/pr500253j ] [PMID: 24762205]
[174]
Steurer, S.; Borkowski, C.; Odinga, S.; Buchholz, M.; Koop, C.; Huland, H.; Becker, M.; Witt, M.; Trede, D.; Omidi, M.; Kraus, O.; Bahar, A.S.; Seddiqi, A.S.; Singer, J.M.; Kwiatkowski, M.; Trusch, M.; Simon, R.; Wurlitzer, M.; Minner, S.; Schlomm, T.; Sauter, G.; Schlüter, H. MALDI mass spectrometric imaging based identification of clinically relevant signals in prostate cancer using large-scale tissue microarrays. Int. J. Cancer, 2013, 133(4), 920-928.
[http://dx.doi.org/10.1002/ijc.28080 ] [PMID: 23381989]
[175]
Kurreck, A.; Vandergrift, L.A.; Fuss, T.L.; Habbel, P.; Agar, N.Y.R.; Cheng, L.L. Prostate cancer diagnosis and characterization with mass spectrometry imaging. Prostate Cancer Prostatic Dis., 2018, 21, 297-305. [https s://doi.org/10.1038/s41391-017-0011-z
[176]
Panderi, I.; Yakirevich, E.; Papagerakis, S.; Noble, L.; Lombardo, K.; Pantazatos, D. Differentiating tumor heterogeneity in formalin-fixed paraffin-embedded (FFPE) prostate adenocarcinoma tissues using principal component analysis of matrix-assisted laser desorption/ionization imaging mass spectral data. Rapid Commun. Mass Spectrom., 2017, 31(2), 160-170.
[http://dx.doi.org/10.1002/rcm.7776 ] [PMID: 27791282]
[177]
Lazova, R.; Seeley, E.H.; Kutzner, H.; Scolyer, R.A.; Scott, G.; Cerroni, L.; Fried, I.; Kozovska, M.E.; Rosenberg, A.S.; Prieto, V.G.; Shehata, B.M.; Durham, M.M.; Henry, G.; Rodriguez-Peralto, J.L.; Riveiro-Falkenbach, E.; Schaefer, J.T.; Danialan, R.; Fraitag, S.; Vollenweider-Roten, S.; Sepehr, A.; Sangueza, M.; Hijazi, N.; Corredoira, Y.; Kowal, R.; Harris, O.M.; Bravo, F.; Boyd, A.S.; Gueorguieva, R.; Caprioli, R.M. Imaging mass spectrometry assists in the classification of diagnostically challenging atypical Spitzoid neoplasms. J. Am. Acad. Dermatol., 2016, 75(6), 1176-1186.e4.
[http://dx.doi.org/10.1016/j.jaad.2016.07.007 ] [PMID: 27502312]
[178]
Guran, R.; Vanickova, L.; Horak, V.; Krizkova, S.; Michalek, P.; Heger, Z.; Zitka, O.; Adam, V. MALDI MSI of MeLiM melanoma: Searching for differences in protein profiles. PLoS One, 2017, 12(12)e0189305
[http://dx.doi.org/10.1371/journal.pone.0189305 ] [PMID: 29220390]
[179]
Vanickova, L. Mass spectrometric imaging of cysteine rich proteins in human skin. Int. J. Biol. Macromol., 2019, 125, 270-277. [PMID: 30517841
[180]
Hardesty, W.M.; Kelley, M.C.; Mi, D.; Low, R.L.; Caprioli, R.M. Protein signatures for survival and recurrence in metastatic melanoma. J. Proteomics, 2011, 74(7), 1002-1014.
[http://dx.doi.org/10.1016/j.jprot.2011.04.013 ] [PMID: 21549228]
[181]
Balluff, B.; Rauser, S.; Meding, S.; Elsner, M.; Schöne, C.; Feuchtinger, A.; Schuhmacher, C.; Novotny, A.; Jütting, U.; Maccarrone, G.; Sarioglu, H.; Ueffing, M.; Braselmann, H.; Zitzelsberger, H.; Schmid, R.M.; Höfler, H.; Ebert, M.P.; Walch, A. MALDI imaging identifies prognostic seven-protein signature of novel tissue markers in intestinal-type gastric cancer. Am. J. Pathol., 2011, 179(6), 2720-2729.
[http://dx.doi.org/10.1016/j.ajpath.2011.08.032 ] [PMID: 22015459]
[182]
Gemoll, T.; Strohkamp, S.; Schillo, K.; Thorns, C.; Habermann, J.K. MALDI-imaging reveals thymosin beta-4 as an independent prognostic marker for colorectal cancer. Oncotarget, 2015, 6(41), 43869-43880.
[http://dx.doi.org/10.18632/oncotarget.6103 ] [PMID: 26556858]
[183]
Steurer, S.; Seddiqi, A.S.; Singer, J.M.; Bahar, A.S.; Eichelberg, C.; Rink, M.; Dahlem, R.; Huland, H.; Sauter, G.; Simon, R.; Minner, S.; Burandt, E.; Stahl, P.R.; Schlomm, T.; Wurlitzer, M.; Schlüter, H. MALDI imaging on tissue microarrays identifies molecular features associated with renal cell cancer phenotype. Anticancer Res., 2014, 34(5), 2255-2261. [PMID: 24778028
[184]
Na, C.H.; Hong, J.H.; Kim, W.S.; Shanta, S.R.; Bang, J.Y.; Park, D.; Kim, H.K.; Kim, K.P. Identification of Protein Markers Specific for Papillary Renal Cell Carcinoma Using Imaging Mass Spectrometry. Mol. Cells, 2015, 38(7), 624-629.
[http://dx.doi.org/10.14348/molcells.2015.0013 ] [PMID: 26062552]
[185]
Prentice, B.M.; Caprioli, R.M.; Vuiblet, V. Label-free molecular imaging of the kidney. Kidney Int., 2017, 92(3), 580-598.
[http://dx.doi.org/10.1016/j.kint.2017.03.052 ] [PMID: 28750926]
[186]
Calligaris, D.; Feldman, D.R.; Norton, I.; Olubiyi, O.; Changelian, A.N.; Machaidze, R.; Vestal, M.L.; Laws, E.R.; Dunn, I.F.; Santagata, S.; Agar, N.Y. MALDI mass spectrometry imaging analysis of pituitary adenomas for near-real-time tumor delineation. Proc. Natl. Acad. Sci. USA, 2015, 112(32), 9978-9983.
[http://dx.doi.org/10.1073/pnas.1423101112 ] [PMID: 26216958]
[187]
Min, K-W.; Bang, J.Y.; Kim, K.P.; Kim, W.S.; Lee, S.H.; Shanta, S.R.; Lee, J.H.; Hong, J.H.; Lim, S.D.; Yoo, Y.B.; Na, C.H. Imaging mass spectrometry in papillary thyroid carcinoma for the identification and validation of biomarker proteins. J. Korean Med. Sci., 2014, 29(7), 934-940.
[http://dx.doi.org/10.3346/jkms.2014.29.7.934 ] [PMID: 25045225]
[188]
Pietrowska, M.; Diehl, H.C.; Mrukwa, G.; Kalinowska-Herok, M.; Gawin, M.; Chekan, M.; Elm, J.; Drazek, G.; Krawczyk, A.; Lange, D.; Meyer, H.E.; Polanska, J.; Henkel, C.; Widlak, P. Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 837-845.
[http://dx.doi.org/10.1016/j.bbapap.2016.10.006 ] [PMID: 27760391]
[189]
Tsypin, M.; Asmellash, S.; Meyer, K.; Touchet, B.; Roder, H. Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis. PLoS One, 2019, 14(12), e0226012-e0226012.
[http://dx.doi.org/10.1371/journal.pone.0226012 ] [PMID: 31815946]
[190]
Maltseva, A. Application of MALDI-MSI for detection of antimicrobial peptides in tissues of the marine invertebrate Arenicola marina. Inverteb. Surv. J., 2016, 13, 205-209.
[191]
Baumann, T.; Kämpfer, U.; Schürch, S.; Schaller, J.; Largiadèr, C.; Nentwig, W.; Kuhn-Nentwig, L. Ctenidins: antimicrobial glycine-rich peptides from the hemocytes of the spider Cupiennius salei. Cell. Mol. Life Sci., 2010, 67(16), 2787-2798. [PMID: 20369272
[http://dx.doi.org/10.1007/s00018-010-0364-0]
[192]
Kuhn-Nentwig, L.; Kopp, L.S.; Nentwig, W.; Haenni, B.; Streitberger, K.; Schürch, S.; Schaller, J. Functional differentiation of spider hemocytes by light and transmission electron microscopy, and MALDI-MS-imaging. Dev. Comp. Immunol., 2014, 43(1), 59-67.
[http://dx.doi.org/10.1016/j.dci.2013.10.008 ] [PMID: 24183821]
[193]
Propheter, D.C.; Hooper, L.V. Bacteria Come into Focus: New Tools for Visualizing the Microbiota. Cell Host Microbe, 2015, 18(4), 392-394.
[http://dx.doi.org/10.1016/j.chom.2015.10.004 ] [PMID: 26468742]
[194]
Qin, L.; Zhang, Y.; Liu, Y.; He, H.; Han, M.; Li, Y.; Zeng, M.; Wang, X. Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants. Phytochem. Anal., 2018, 29(4), 351-364.
[http://dx.doi.org/10.1002/pca.2759 ] [PMID: 29667236]
[195]
Green-Mitchell, S.M.; Cazares, L.H.; Semmes, O.J.; Nadler, J.L.; Nyalwidhe, J.O. On-tissue identification of insulin: in situ reduction coupled with mass spectrometry imaging. Proteomics Clin. Appl., 2011, 5(7-8), 448-453.
[http://dx.doi.org/10.1002/prca.201000152 ] [PMID: 21656913]
[196]
Schulz, S.; Römpp, A.; Kummer, W.; Spengler, B. AP-MALDI imaging of neuropeptides in mouse pituitary gland with 5?? m spatial resolution and high mass accuracy. Int. J. Mass Spectrom., 2011, 305, 228-237.
[http://dx.doi.org/10.1016/j.ijms.2010.11.011.]]
[197]
de Macedo, C.S.; Anderson, D.M.; Schey, K.L. MALDI (matrix assisted laser desorption ionization) Imaging Mass Spectrometry (IMS) of skin: Aspects of sample preparation. Talanta, 2017, 174, 325-335.
[http://dx.doi.org/10.1016/j.talanta.2017.06.018 ] [PMID: 28738588]
[198]
Taverna, D.; Nanney, L.B.; Pollins, A.C.; Sindona, G.; Caprioli, R. Spatial mapping by imaging mass spectrometry offers advancements for rapid definition of human skin proteomic signatures. Exp. Dermatol., 2011, 20(8), 642-647.
[http://dx.doi.org/10.1111/j.1600-0625.2011.01289.x ] [PMID: 21545539]
[199]
Angel, P.M.; Comte-Walters, S.; Ball, L.E.; Talbot, K.; Mehta, A.; Brockbank, K.G.M.; Drake, R.R. Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry. J. Proteome Res., 2018, 17(1), 635-646.
[http://dx.doi.org/10.1021/acs.jproteome.7b00713 ] [PMID: 29161047]
[200]
Brunetti, A.E.; Marani, M.M.; Soldi, R.A.; Mendonça, J.N.; Faivovich, J.; Cabrera, G.M.; Lopes, N.P. Cleavage of Peptides from Amphibian Skin Revealed by Combining Analysis of Gland Secretion and in Situ MALDI Imaging Mass Spectrometry. ACS Omega, 2018, 3(5), 5426-5434.
[http://dx.doi.org/10.1021/acsomega.7b02029 ] [PMID: 30023919]
[201]
Harvey, A.; Cole, L.M.; Day, R.; Bartlett, M.; Warwick, J.; Bojar, R.; Smith, D.; Cross, N.; Clench, M.R. MALDI-MSI for the analysis of a 3D tissue-engineered psoriatic skin model. Proteomics, 2016, 16(11-12), 1718-1725.
[http://dx.doi.org/10.1002/pmic.201600036 ] [PMID: 27226230]
[202]
Nilsson, A.; Peric, A.; Strimfors, M.; Goodwin, R.J.A.; Hayes, M.A.; Andrén, P.E.; Hilgendorf, C. Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis. Sci. Rep., 2017, 7(1), 6352.
[http://dx.doi.org/10.1038/s41598-017-06583-4 ] [PMID: 28743866]
[203]
Klein, O.; Strohschein, K.; Nebrich, G.; Oetjen, J.; Trede, D.; Thiele, H.; Alexandrov, T.; Giavalisco, P.; Duda, G.N.; von Roth, P.; Geissler, S.; Klose, J.; Winkler, T. MALDI imaging mass spectrometry: discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures. Proteomics, 2014, 14(20), 2249-2260.
[http://dx.doi.org/10.1002/pmic.201400088 ] [PMID: 25056804]
[204]
Körner, A. MALDI MS in Analysis of Keratin Fibre Proteins.Applications of Mass Spectrometry in Life Safety. NATO Science for Peace and Security Series A: Chemistry and Biology; Popescu, C.; Zamfir, A.D.; Dinca, N., Eds.; Springer: Dordrecht, 2008. [https s://doi.org/10.1007/978-1-4020-8811-7_14]
[205]
Lalowski, M.; Magni, F.; Mainini, V.; Monogioudi, E.; Gotsopoulos, A.; Soliymani, R.; Chinello, C.; Baumann, M. Imaging mass spectrometry: a new tool for kidney disease investigations. Nephrol. Dial. Transplant., 2013, 28(7), 1648-1656.
[http://dx.doi.org/10.1093/ndt/gft008 ] [PMID: 23553250]
[206]
Magni, F. Proteomics imaging and the kidney. J. Nephrol., 2013, 26(3), 430-436.
[207]
Smith, A.; L’Imperio, V.; De Sio, G.; Ferrario, F.; Scalia, C.; Dell’Antonio, G.; Pieruzzi, F.; Pontillo, C.; Filip, S.; Markoska, K.; Granata, A.; Spasovski, G.; Jankowski, J.; Capasso, G.; Pagni, F.; Magni, F. α-1-Antitrypsin detected by MALDI imaging in the study of glomerulonephritis: Its relevance in chronic kidney disease progression. Proteomics, 2016, 16(11-12), 1759-1766.
[http://dx.doi.org/10.1002/pmic.201500411 ] [PMID: 26749278]
[208]
Smith, A.; L’Imperio, V.; Ajello, E.; Ferrario, F.; Mosele, N.; Stella, M.; Galli, M.; Chinello, C.; Pieruzzi, F.; Spasovski, G.; Pagni, F.; Magni, F. The putative role of MALDI-MSI in the study of Membranous Nephropathy. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(7), 865-874.
[http://dx.doi.org/10.1016/j.bbapap.2016.11.013 ] [PMID: 27890680]
[209]
Winter, M.; Tholey, A.; Kristen, A.; Röcken, C. MALDI Mass Spectrometry Imaging: A Novel Tool for the Identification and Classification of Amyloidosis. Proteomics, 2017, 17(22)1700236
[http://dx.doi.org/10.1002/pmic.201700236 ] [PMID: 28994248]
[210]
Oliva, R.; Martínez-Heredia, J.; Estanyol, J.M. Proteomics in the study of the sperm cell composition, differentiation and function. Syst Biol Reprod Med, 2008, 54(1), 23-36.
[http://dx.doi.org/10.1080/19396360701879595 ] [PMID: 18543863]
[211]
Lagarrigue, M.; Lavigne, R.; Guével, B.; Com, E.; Chaurand, P.; Pineau, C. 2012.
[212]
Lagarrigue, M.; Becker, M.; Lavigne, R.; Deininger, S.-O.; Walch, A.; Aubry, F.; Suckau, D.; Pineau, C. 2011.
[213]
Venkatraman, A.; Hochart, G.; Bonnel, D.; Stauber, J.; Shimmura, S.; Rajamani, L.; Pervushin, K.; Mehta, J.S. Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging of Key Proteins in Corneal Samples from Lattice Dystrophy Patients with TGFBI-H626R and TGFBI-R124C Mutations. Proteomics Clin. Appl., 2019, 13(1)e1800053
[http://dx.doi.org/10.1002/prca.201800053 ] [PMID: 30387319]
[214]
Schulz, S.; Becker, M.; Groseclose, M.R.; Schadt, S.; Hopf, C. Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development. Curr. Opin. Biotechnol., 2019, 55, 51-59.
[http://dx.doi.org/10.1016/j.copbio.2018.08.003 ] [PMID: 30153614]
[215]
Bateman, N.W.; Goulding, S.P.; Shulman, N.J.; Gadok, A.K.; Szumlinski, K.K.; MacCoss, M.J.; Wu, C.C. Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA). Mol. Cell. Proteomics, 2014, 13(1), 329-338.
[http://dx.doi.org/10.1074/mcp.M112.026500 ] [PMID: 23820513]
[216]
Neilson, K.A.; Ali, N.A.; Muralidharan, S.; Mirzaei, M.; Mariani, M.; Assadourian, G.; Lee, A.; van Sluyter, S.C.; Haynes, P.A. Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics, 2011, 11(4), 535-553.
[http://dx.doi.org/10.1002/pmic.201000553 ] [PMID: 21243637]
[217]
Tabb, D.L.; Vega-Montoto, L.; Rudnick, P.A.; Variyath, A.M.; Ham, A.J.; Bunk, D.M.; Kilpatrick, L.E.; Billheimer, D.D.; Blackman, R.K.; Cardasis, H.L.; Carr, S.A.; Clauser, K.R.; Jaffe, J.D.; Kowalski, K.A.; Neubert, T.A.; Regnier, F.E.; Schilling, B.; Tegeler, T.J.; Wang, M.; Wang, P.; Whiteaker, J.R.; Zimmerman, L.J.; Fisher, S.J.; Gibson, B.W.; Kinsinger, C.R.; Mesri, M.; Rodriguez, H.; Stein, S.E.; Tempst, P.; Paulovich, A.G.; Liebler, D.C.; Spiegelman, C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res., 2010, 9(2), 761-776.
[http://dx.doi.org/10.1021/pr9006365 ] [PMID: 19921851]
[218]
Liu, H.; Sadygov, R.G.; Yates, J.R. III A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem., 2004, 76(14), 4193-4201.
[http://dx.doi.org/10.1021/ac0498563 ] [PMID: 15253663]
[219]
Sang, S.; Lee, M.J.; Yang, I.; Buckley, B.; Yang, C.S. Human urinary metabolite profile of tea polyphenols analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry with data-dependent acquisition. Rapid Commun. Mass Spectrom., 2008, 22(10), 1567-1578.
[http://dx.doi.org/10.1002/rcm.3546 ] [PMID: 18433082]
[220]
Thoren, K.L.; Colby, J.M.; Shugarts, S.B.; Wu, A.H.; Lynch, K.L. Comparison of Information-Dependent Acquisition on a Tandem Quadrupole TOF vs a Triple Quadrupole Linear Ion Trap Mass Spectrometer for Broad-Spectrum Drug Screening. Clin. Chem., 2016, 62(1), 170-178.
[http://dx.doi.org/10.1373/clinchem.2015.241315 ] [PMID: 26453698]
[221]
Scholz, K.; Dekant, W.; Völkel, W.; Pähler, A. Rapid detection and identification of N-acetyl-L-cysteine thioethers using constant neutral loss and theoretical multiple reaction monitoring combined with enhanced product-ion scans on a linear ion trap mass spectrometer. J. Am. Soc. Mass Spectrom., 2005, 16(12), 1976-1984.
[http://dx.doi.org/10.1016/j.jasms.2005.08.003 ] [PMID: 16246572]
[222]
Villén, J.; Beausoleil, S.A.; Gygi, S.P. Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics, 2008, 8(21), 4444-4452.
[http://dx.doi.org/10.1002/pmic.200800283 ] [PMID: 18972524]
[223]
Sokolowska, I.; Ngounou Wetie, A.G.; Roy, U.; Woods, A.G.; Darie, C.C. Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochim. Biophys. Acta, 2013, 1834(8), 1474-1483.
[http://dx.doi.org/10.1016/j.bbapap.2013.04.022 ] [PMID: 23632316]
[224]
Doerr, A. DIA mass spectrometry. Nat. Methods, 2015, 12(1), 35-35.
[http://dx.doi.org/10.1038/nmeth.3234 ] [PMID: 25699317]
[225]
Plumb, R.S.; Johnson, K.A.; Rainville, P.; Smith, B.W.; Wilson, I.D.; Castro-Perez, J.M.; Nicholson, J.K. UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom., 2006, 20(13), 1989-1994.
[http://dx.doi.org/10.1002/rcm.2550 ] [PMID: 16755610]
[226]
Moran, D.; Cross, T.; Brown, L.M.; Colligan, R.M.; Dunbar, D. Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J. Virol. Methods, 2014, 195, 9-17.
[http://dx.doi.org/10.1016/j.jviromet.2013.10.007 ] [PMID: 24129072]
[227]
Ge, H. Label free quantitative proteomics of formalin fixed embedded (FFPE) tissue sections from temporal giant cell arteritis patients. Proceedings of the 59th annual conference on mass spectrometry and allied topics, 2011.
[228]
Ibrahim, Y. Performance of a new sensitive LC-IMS-QTOF platform for proteomics measurements. Proceedings of the 59th annual conference on mass spectrometry and allied topics, 2011.
[229]
Lange, V.; Picotti, P.; Domon, B.; Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol., 2008, 4, 222-222.
[http://dx.doi.org/10.1038/msb.2008.61 ] [PMID: 18854821]
[230]
Stone, P. New dynamic MRM mode improves data quality and triple quad quantification in complex analyses., 2009.
[231]
Matraszek-Zuchowska, I.; Wozniak, B.; Posyniak, A. Comparison of the Multiple Reaction Monitoring and Enhanced Product Ion Scan Modes for Confirmation of Stilbenes in Bovine Urine Samples Using LC-MS/MS QTRAP® System. Chromatographia, 2016, 79, 1003-1012.
[http://dx.doi.org/10.1007/s10337-016-3121-1 ] [PMID: 27512157]
[232]
Rauniyar, N. Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int. J. Mol. Sci., 2015, 16(12), 28566-28581.
[http://dx.doi.org/10.3390/ijms161226120 ] [PMID: 26633379]
[233]
Gallien, S.; Duriez, E.; Crone, C.; Kellmann, M.; Moehring, T.; Domon, B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics, 2012, 11(12), 1709-1723.
[http://dx.doi.org/10.1074/mcp.O112.019802 ] [PMID: 22962056]
[234]
Li, S.; Nakayama, T.; Akinc, A.; Wu, S.L.; Karger, B.L. Development of LC-MS methods for quantitation of hepcidin and demonstration of siRNA-mediated hepcidin suppression in serum. J. Pharmacol. Toxicol. Methods, 2015, 71, 110-119.
[http://dx.doi.org/10.1016/j.vascn.2014.09.008 ] [PMID: 25281793]
[235]
Nagaraj, N.; Wisniewski, J.R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Pääbo, S.; Mann, M. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol., 2011, 7, 548-548.
[http://dx.doi.org/10.1038/msb.2011.81 ] [PMID: 22068331]
[236]
Geiger, T. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins., 2012.
[237]
Michalski, A.; Cox, J.; Mann, M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res., 2011, 10(4), 1785-1793.
[http://dx.doi.org/10.1021/pr101060v ] [PMID: 21309581]
[238]
Vollmer, M.; Hörth, P.; Nägele, E. Optimization of two-dimensional off-line LC/MS separations to improve resolution of complex proteomic samples. Anal. Chem., 2004, 76(17), 5180-5185.
[http://dx.doi.org/10.1021/ac040022u ] [PMID: 15373459]
[239]
Ivanov, A.R.; Zang, L.; Karger, B.L.; Low-Attomole Electrospray Ionization, M.S. Low-attomole electrospray ionization MS and MS/MS analysis of protein tryptic digests using 20-microm-i.d. polystyrene-divinylbenzene monolithic capillary columns. Anal. Chem., 2003, 75(20), 5306-5316.
[http://dx.doi.org/10.1021/ac030163g ] [PMID: 14710807]
[240]
Keshishian, H.; Burgess, M.W.; Specht, H.; Wallace, L.; Clauser, K.R.; Gillette, M.A.; Carr, S.A. Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry. Nat. Protoc., 2017, 12(8), 1683-1701.
[http://dx.doi.org/10.1038/nprot.2017.054 ] [PMID: 28749931]
[241]
Thakur, S.S. Deep and highly sensitive proteome coverage by LCMS/ MS without prefractionation. Mol. Cell. Proteomics, 2011, 10(8), M1.
[http://dx.doi.org/10.003699.]]
[242]
Hsieh, E.J.; Bereman, M.S.; Durand, S.; Valaskovic, G.A.; MacCoss, M.J. Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples. J. Am. Soc. Mass Spectrom., 2013, 24(1), 148-153.
[http://dx.doi.org/10.1007/s13361-012-0508-6 ] [PMID: 23197307]
[243]
Kulak, N.A.; Pichler, G.; Paron, I.; Nagaraj, N.; Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat. Methods, 2014, 11(3), 319-324.
[http://dx.doi.org/10.1038/nmeth.2834 ] [PMID: 24487582]
[244]
Moruz, L.; Pichler, P.; Stranzl, T.; Mechtler, K.; Käll, L. Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics. Anal. Chem., 2013, 85(16), 7777-7785.
[http://dx.doi.org/10.1021/ac401145q ] [PMID: 23841592]
[245]
Köcher, T.; Swart, R.; Mechtler, K. Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem., 2011, 83(7), 2699-2704.
[http://dx.doi.org/10.1021/ac103243t ] [PMID: 21388192]
[246]
Trudgian, D.C.; Fischer, R.; Guo, X.; Kessler, B.M.; Mirzaei, H. GOAT--a simple LC-MS/MS gradient optimization tool. Proteomics, 2014, 14(12), 1467-1471.
[http://dx.doi.org/10.1002/pmic.201300524 ] [PMID: 24723505]
[247]
Branca, R.M.M.; Orre, L.M.; Johansson, H.J.; Granholm, V.; Huss, M.; Pérez-Bercoff, Å.; Forshed, J.; Käll, L.; Lehtiö, J. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat. Methods, 2014, 11(1), 59-62.
[http://dx.doi.org/10.1038/nmeth.2732 ] [PMID: 24240322]
[248]
Zhou, F.; Lu, Y.; Ficarro, S.B.; Adelmant, G.; Jiang, W.; Luckey, C.J.; Marto, J.A. Genome-scale proteome quantification by DEEP SEQ mass spectrometry. Nat. Commun., 2013, 4(2171), 2171.
[http://dx.doi.org/10.1038/ncomms3171 ] [PMID: 23863870]
[249]
Wang, H.; Yang, Y.; Li, Y.; Bai, B.; Wang, X.; Tan, H.; Liu, T.; Beach, T.G.; Peng, J.; Wu, Z. Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome. J. Proteome Res., 2015, 14(2), 829-838.
[http://dx.doi.org/10.1021/pr500882h ] [PMID: 25455107]
[250]
Kuster, B.; Schirle, M.; Mallick, P.; Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol., 2005, 6(7), 577-583.
[http://dx.doi.org/10.1038/nrm1683 ] [PMID: 15957003]
[251]
Makarov, A.; Denisov, E.; Lange, O. Performance evaluation of a high-field Orbitrap mass analyzer. J. Am. Soc. Mass Spectrom., 2009, 20(8), 1391-1396.
[http://dx.doi.org/10.1016/j.jasms.2009.01.005 ] [PMID: 19216090]
[252]
Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 2008, 26(12), 1367-1372.
[http://dx.doi.org/10.1038/nbt.1511 ] [PMID: 19029910]
[253]
Alves, G.; Ogurtsov, A.Y.; Kwok, S.; Wu, W.W.; Wang, G.; Shen, R.F.; Yu, Y.K. Detection of co-eluted peptides using database search methods. Biol. Direct, 2008, 3, 27-27.
[http://dx.doi.org/10.1186/1745-6150-3-27 ] [PMID: 18597684]
[254]
Aburaya, S.; Aoki, W.; Minakuchi, H.; Ueda, M. Definitive screening design enables optimization of LC-ESI-MS/MS parameters in proteomics. Biosci. Biotechnol. Biochem., 2017, 81(12), 2237-2243.
[http://dx.doi.org/10.1080/09168451.2017.1391685 ] [PMID: 29068257]
[255]
Nie, L.; Zhu, M.; Sun, S.; Zhai, L.; Wu, Z.; Qiana, L.; Tan, M. An optimization of the LC-MS/MS workflow for deep proteome profiling on an Orbitrap Fusion. Anal. Methods, 2016, 8, 425-434.
[http://dx.doi.org/10.1039/C5AY01900A]]
[256]
Tuli, L.; Tsai, T.H.; Varghese, R.S.; Xiao, J.F.; Cheema, A.; Ressom, H.W. Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Sci., 2012, 10(1), 13.
[http://dx.doi.org/10.1186/1477-5956-10-13 ] [PMID: 22369182]
[257]
Välikangas, T.; Suomi, T.; Elo, L.L. A systematic evaluation of normalization methods in quantitative label-free proteomics. Brief. Bioinform., 2018, 19(1), 1-11. [PMID: 27694351
[258]
Nagaraj, S.H.; Gasser, R.B.; Ranganathan, S. A hitchhiker’s guide to expressed sequence tag (EST) analysis. Brief. Bioinform., 2007, 8(1), 6-21.
[http://dx.doi.org/10.1093/bib/bbl015 ] [PMID: 16772268]
[259]
Nesvizhskii, A.I. Proteogenomics: concepts, applications and computational strategies. Nat. Methods, 2014, 11(11), 1114-1125.
[http://dx.doi.org/10.1038/nmeth.3144 ] [PMID: 25357241]
[260]
Ma, B.; Zhang, K.; Hendrie, C.; Liang, C.; Li, M.; Doherty-Kirby, A.; Lajoie, G. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom., 2003, 17(20), 2337-2342.
[http://dx.doi.org/10.1002/rcm.1196 ] [PMID: 14558135]
[261]
Taylor, J.A.; Johnson, R.S. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom., 1997, 11(9), 1067-1075.
[http://dx.doi.org/10.1002/(SICI)1097- 0231(19970615)11:9<1067: AID-RCM953>3.0.CO;2-L ] [PMID: 9204580]
[262]
Frank, A.; Pevzner, P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem., 2005, 77(4), 964-973.
[http://dx.doi.org/10.1021/ac048788h ] [PMID: 15858974]
[263]
Kalb, S.R.; Baudys, J.; Rees, J.C.; Smith, T.J.; Smith, L.A.; Helma, C.H.; Hill, K.; Kull, S.; Kirchner, S.; Dorner, M.B.; Dorner, B.G.; Pirkle, J.L.; Barr, J.R. De novo subtype and strain identification of botulinum neurotoxin type B through toxin proteomics. Anal. Bioanal. Chem., 2012, 403(1), 215-226.
[http://dx.doi.org/10.1007/s00216-012-5767-3 ] [PMID: 22395449]
[264]
Medzihradszky, K.F.; Chalkley, R.J. Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spectrom. Rev., 2015, 34(1), 43-63.
[http://dx.doi.org/10.1002/mas.21406 ] [PMID: 25667941]
[265]
Ma, B. Novor: real-time peptide de novo sequencing software. J. Am. Soc. Mass Spectrom., 2015, 26(11), 1885-1894.
[http://dx.doi.org/10.1007/s13361-015-1204-0 ] [PMID: 26122521]
[266]
Sadygov, R.G. Using SEQUEST with theoretically complete sequence databases. J. Am. Soc. Mass Spectrom., 2015, 26(11), 1858-1864.
[http://dx.doi.org/10.1007/s13361-015-1228-5 ] [PMID: 26238326]
[267]
Jeong, K.; Kim, S.; Pevzner, P.A. UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics, 2013, 29(16), 1953-1962.
[http://dx.doi.org/10.1093/bioinformatics/btt338 ] [PMID: 23766417]
[268]
Eng, J.K.; Hoopmann, M.R.; Jahan, T.A.; Egertson, J.D.; Noble, W.S.; MacCoss, M.J. A deeper look into Comet--implementation and features. J. Am. Soc. Mass Spectrom., 2015, 26(11), 1865-1874.
[http://dx.doi.org/10.1007/s13361-015-1179-x ] [PMID: 26115965]
[269]
Keller, A.; Nesvizhskii, A.I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem., 2002, 74(20), 5383-5392.
[http://dx.doi.org/10.1021/ac025747h ] [PMID: 12403597]
[270]
Vehus, T. Performing Quantitative Determination of LowAbundant Proteins by Targeted Mass Spectrometry Liquid Chromatography, 2017.

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy