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Volumn 26, Issue 1, 2014, Pages 44-54

XMS: Cross-platform normalization method for multimodal mass spectrometric tissue profiling

Author keywords

Algorithm; Correlation; Cross platform normalization; Desorption electrospray ionization; Desorption ionization mass spectrometry; k Nearest neighbor; Laser desorption ionization; Lipids; Mass spectrometry; Peak annotation; Principal component analysis; Rapid evaporative ionization mass spectrometry

Indexed keywords

ALGORITHMS; CORRELATION METHODS; DESORPTION; ELECTROSPRAY IONIZATION; FOURIER TRANSFORMS; IONIZATION; LIPIDS; MASS SPECTROMETERS; MASS SPECTROMETRY; MOLECULAR GRAPHICS; NATURAL LANGUAGE PROCESSING SYSTEMS; PRINCIPAL COMPONENT ANALYSIS; TISSUE;

EID: 84919906679     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-014-0997-6     Document Type: Article
Times cited : (10)

References (39)
  • 1
    • 52649174783 scopus 로고    scopus 로고
    • Established and emerging atmospheric pressure surface sampling/ionization techniques for mass spectrometry
    • Van Berkel, G.J.; Pasilis, S.P.; Ovchinnikova, O.: Established and emerging atmospheric pressure surface sampling/ionization techniques for mass spectrometry. J. Mass Spectrom. 43, 1161-1180 (2008)
    • (2008) J. Mass Spectrom. , vol.43 , pp. 1161-1180
    • Van Berkel, G.J.1    Pasilis, S.P.2    Ovchinnikova, O.3
  • 2
    • 36849106204 scopus 로고
    • Ion microprobe mass analyzer
    • 1:CAS:528:DyaF1cXktFertQ%3D%3D 10.1063/1.1709314
    • Liebl, H.: Ion microprobe mass analyzer. J. Appl. Phys. 38, 5277-5283 (1967)
    • (1967) J. Appl. Phys. , vol.38 , pp. 5277-5283
    • Liebl, H.1
  • 3
    • 5644249240 scopus 로고    scopus 로고
    • Mass spectrometry sampling under ambient conditions with desorption electrospray ionization
    • 1:CAS:528:DC%2BD2cXotlCkt7s%3D 10.1126/science.1104404
    • Takats, Z.; Wiseman, J.M.; Gologan, B.; Cooks, R.G.: Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 306, 471-473 (2004)
    • (2004) Science , vol.306 , pp. 471-473
    • Takats, Z.1    Wiseman, J.M.2    Gologan, B.3    Cooks, R.G.4
  • 4
    • 24644477568 scopus 로고
    • Matrix-assisted ultraviolet-laser desorption of nonvolatile compounds
    • 1:CAS:528:DyaL2sXmsVGqsrg%3D 10.1016/0168-1176(87)87041-6
    • Karas, M.; Bachmann, D.; Bahr, U.; Hillenkamp, F.: Matrix-assisted ultraviolet-laser desorption of nonvolatile compounds. Int. J. Mass Spectrom. Ion Process 78, 53-68 (1987)
    • (1987) Int. J. Mass Spectrom. Ion Process , vol.78 , pp. 53-68
    • Karas, M.1    Bachmann, D.2    Bahr, U.3    Hillenkamp, F.4
  • 5
    • 0031304362 scopus 로고    scopus 로고
    • Molecular imaging of biological samples: Localization of peptides and proteins using MALDI-TOF MS
    • 1:CAS:528:DyaK2sXntVagtLc%3D 10.1021/ac970888i
    • Caprioli, R.M.; Farmer, T.B.; Gile, J.: Molecular imaging of biological samples: Localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 69, 4751-4760 (1997)
    • (1997) Anal. Chem. , vol.69 , pp. 4751-4760
    • Caprioli, R.M.1    Farmer, T.B.2    Gile, J.3
  • 6
    • 77952664027 scopus 로고    scopus 로고
    • Histology by mass spectrometry: Label-free tissue characterization obtained from high-accuracy bioanalytical imaging
    • Rompp, A.; Guenther, S.; Schober, Y.; Schulz, O.; Takats, Z.; Kummer, W.; Spengler, B.: Histology by mass spectrometry: Label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew. Chem. Int. Ed. 49, 3834-3838 (2010)
    • (2010) Angew. Chem. Int. Ed. , vol.49 , pp. 3834-3838
    • Rompp, A.1    Guenther, S.2    Schober, Y.3    Schulz, O.4    Takats, Z.5    Kummer, W.6    Spengler, B.7
  • 7
    • 35848970035 scopus 로고    scopus 로고
    • MALDI imaging mass spectrometry: Molecular snapshots of biochemical systems
    • 1:CAS:528:DC%2BD2sXhtV2mtr7F 10.1038/nmeth1094
    • Cornett, D.S.; Reyzer, M.L.; Chaurand, P.; Caprioli, R.M.: MALDI imaging mass spectrometry: Molecular snapshots of biochemical systems. Nat. Methods 4, 828-833 (2007)
    • (2007) Nat. Methods , vol.4 , pp. 828-833
    • Cornett, D.S.1    Reyzer, M.L.2    Chaurand, P.3    Caprioli, R.M.4
  • 8
    • 50249147732 scopus 로고    scopus 로고
    • MALDI imaging mass spectrometry for direct tissue analysis: A new frontier for molecular histology
    • 1:CAS:528:DC%2BD1cXhtVWns7jN 10.1007/s00418-008-0469-9
    • Walch, A.; Rauser, S.; Deininger, S.O.; Höfler, H.: MALDI imaging mass spectrometry for direct tissue analysis: A new frontier for molecular histology. Histochem. Cell Biol. 130, 421-434 (2008)
    • (2008) Histochem. Cell Biol. , vol.130 , pp. 421-434
    • Walch, A.1    Rauser, S.2    Deininger, S.O.3    Höfler, H.4
  • 9
    • 77955952166 scopus 로고    scopus 로고
    • Molecular imaging by mass spectrometry - Looking beyond classical histology
    • 1:CAS:528:DC%2BC3cXhtVCmtbzO 10.1038/nrc2917
    • Schwamborn, K.; Caprioli, R.M.: Molecular imaging by mass spectrometry - looking beyond classical histology. Nat. Rev. Cancer. 10, 639-646 (2010)
    • (2010) Nat. Rev. Cancer. , vol.10 , pp. 639-646
    • Schwamborn, K.1    Caprioli, R.M.2
  • 12
    • 79960559981 scopus 로고    scopus 로고
    • Mass spectrometry imaging with high resolution in mass and space (HR(2) MSI) for reliable investigation of drug compound distributions on the cellular level
    • Rompp, A.; Guenther, S.; Takats, Z.; Spengler, B.: Mass spectrometry imaging with high resolution in mass and space (HR(2) MSI) for reliable investigation of drug compound distributions on the cellular level. Anal. Bioanal. Chem. 401, 65-73 (2011)
    • (2011) Anal. Bioanal. Chem. , vol.401 , pp. 65-73
    • Rompp, A.1    Guenther, S.2    Takats, Z.3    Spengler, B.4
  • 13
    • 84856699971 scopus 로고    scopus 로고
    • Enhanced sensitivity for high spatial resolution lipid analysis by negative ion mode matrix assisted laser desorption ionization imaging mass spectrometry
    • 1:CAS:528:DC%2BC38XivVCmtw%3D%3D 10.1021/ac202383m
    • Angel, P.M.; Spraggins, J.M.; Baldwin, H.S.; Caprioli, R.: Enhanced sensitivity for high spatial resolution lipid analysis by negative ion mode matrix assisted laser desorption ionization imaging mass spectrometry. Anal. Chem. 84, 1557-64 (2012)
    • (2012) Anal. Chem. , vol.84 , pp. 1557-1564
    • Angel, P.M.1    Spraggins, J.M.2    Baldwin, H.S.3    Caprioli, R.4
  • 14
    • 82755195845 scopus 로고    scopus 로고
    • Empirical comparison of cross-platform normalization methods for gene expression data
    • Rudy, J.; Valafar, F.: Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinforma. 12, 467 (2011)
    • (2011) BMC Bioinforma. , vol.12 , pp. 467
    • Rudy, J.1    Valafar, F.2
  • 15
    • 42649134796 scopus 로고    scopus 로고
    • Merging two gene-expression studies via cross-platform normalization
    • 1:CAS:528:DC%2BD1cXlt1agsLs%3D 10.1093/bioinformatics/btn083
    • Shabalin, A.A.; Tjelmeland, H.; Fan, C.; Perou, C.M.; Nobel, A.B.: Merging two gene-expression studies via cross-platform normalization. Bioinformatics 24, 1154-1160 (2008)
    • (2008) Bioinformatics , vol.24 , pp. 1154-1160
    • Shabalin, A.A.1    Tjelmeland, H.2    Fan, C.3    Perou, C.M.4    Nobel, A.B.5
  • 16
    • 0347090327 scopus 로고    scopus 로고
    • Adjustment of systematic microarray data biases
    • 1:CAS:528:DC%2BD2cXns12n 10.1093/bioinformatics/btg385
    • Benito, M.; Parker, J.; Du, Q.; Wu, J.; Xiang, D.; Perou, C.M.; Marron, J.S.: Adjustment of systematic microarray data biases. Bioinformatics 20, 105-114 (2004)
    • (2004) Bioinformatics , vol.20 , pp. 105-114
    • Benito, M.1    Parker, J.2    Du, Q.3    Wu, J.4    Xiang, D.5    Perou, C.M.6    Marron, J.S.7
  • 17
    • 55249088991 scopus 로고    scopus 로고
    • Empirical Bayes accommodation of batch-effects in microarray data using identical replicate reference samples: Application to RNA expression profiling of blood from Duchenne muscular dystrophy patients
    • Walker, W.; Liao, I.; Gilbert, D.; Wong, B.; Pollard, K.; Mcculloch, C.; Lit, L.; Sharp, F.: Empirical Bayes accommodation of batch-effects in microarray data using identical replicate reference samples: Application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics 9, 494 (2008)
    • (2008) BMC Genomics , vol.9 , pp. 494
    • Walker, W.1    Liao, I.2    Gilbert, D.3    Wong, B.4    Pollard, K.5    McCulloch, C.6    Lit, L.7    Sharp, F.8
  • 19
    • 69849112774 scopus 로고    scopus 로고
    • WebArrayDB: Cross-platform microarray data analysis and public data repository
    • 1:CAS:528:DC%2BD1MXhtFSnsrnI 10.1093/bioinformatics/btp430
    • Xia, X.; Mcclelland, M.; Porwollik, S.; Song, W.; Cong, X.; Wang, Y.: WebArrayDB: Cross-platform microarray data analysis and public data repository. Bioinformatics 25, 2425-2429 (2009)
    • (2009) Bioinformatics , vol.25 , pp. 2425-2429
    • Xia, X.1    McClelland, M.2    Porwollik, S.3    Song, W.4    Cong, X.5    Wang, Y.6
  • 20
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 1:CAS:528:DC%2BD3sXitlCnsL4%3D 10.1093/bioinformatics/19.2.185
    • Bolstad, B.; Irizarry, R.; Astrand, M.; Speed, T.: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185 (2003)
    • (2003) Bioinformatics , vol.19 , pp. 185
    • Bolstad, B.1    Irizarry, R.2    Astrand, M.3    Speed, T.4
  • 21
    • 77956265904 scopus 로고    scopus 로고
    • DSGeo: Software tools for cross-platform analysis of gene expression data in GEO
    • 1:CAS:528:DC%2BC3cXhtFWqtbzJ 10.1016/j.jbi.2010.04.007
    • Lacson, R.; Pitzer, E.; Kim, J.; Galante, P.; Hinske, C.; Ohno-Machado, L.: DSGeo: Software tools for cross-platform analysis of gene expression data in GEO. J. Biomed. Inform. 43, 709-715 (2010)
    • (2010) J. Biomed. Inform. , vol.43 , pp. 709-715
    • Lacson, R.1    Pitzer, E.2    Kim, J.3    Galante, P.4    Hinske, C.5    Ohno-Machado, L.6
  • 22
    • 10744233766 scopus 로고    scopus 로고
    • Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
    • 1:CAS:528:DC%2BD3sXmtVKlur0%3D 10.1021/ac026468x
    • Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T.A.; Hill, L.R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C.H.: Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75, 4818-4826 (2003)
    • (2003) Anal. Chem. , vol.75 , pp. 4818-4826
    • Wang, W.1    Zhou, H.2    Lin, H.3    Roy, S.4    Shaler, T.A.5    Hill, L.R.6    Norton, S.7    Kumar, P.8    Anderle, M.9    Becker, C.H.10
  • 23
    • 84865169841 scopus 로고    scopus 로고
    • Quantitative mass spectrometry imaging of propranolol and olanzapine using tissue extinction calculation as normalization factor
    • 1:CAS:528:DC%2BC38XhtFGrtrjM 10.1016/j.jprot.2012.07.035
    • Hamm, G.; Bonnel, D.; Legouffe, R.; Pamelard, F.; Delbos, J.-M.; Bouzom, F.; Stauber, J.: Quantitative mass spectrometry imaging of propranolol and olanzapine using tissue extinction calculation as normalization factor. J. Proteome 75, 4952-4961 (2012)
    • (2012) J. Proteome , vol.75 , pp. 4952-4961
    • Hamm, G.1    Bonnel, D.2    Legouffe, R.3    Pamelard, F.4    Delbos, J.-M.5    Bouzom, F.6    Stauber, J.7
  • 25
    • 78651516935 scopus 로고    scopus 로고
    • A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language
    • R8 1:CAS:528:DC%2BC3MXivVymtrk%3D 10.1186/gb-2011-12-1-r8
    • Herzog, R.; Schwudke, D.; Schuhmann, K.; Sampaio, J.L.; Bornstein, S.R.; Schroeder, M.; Shevchenko, A.: A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 12, R8 (2011)
    • (2011) Genome Biol. , vol.12
    • Herzog, R.1    Schwudke, D.2    Schuhmann, K.3    Sampaio, J.L.4    Bornstein, S.R.5    Schroeder, M.6    Shevchenko, A.7
  • 26
    • 79951541434 scopus 로고    scopus 로고
    • Lipid data analyzer: Unattended identification and quantitation of lipids in LC-MS data
    • 1:CAS:528:DC%2BC3MXitVWgsLk%3D 10.1093/bioinformatics/btq699
    • Hartler, J.; Trötzmüller, M.; Chitraju, C.; Spener, F.; Köfeler, H.C.; Thallinger, G.G.: Lipid data analyzer: Unattended identification and quantitation of lipids in LC-MS data. Bioinformatics 27, 572-577 (2011)
    • (2011) Bioinformatics , vol.27 , pp. 572-577
    • Hartler, J.1    Trötzmüller, M.2    Chitraju, C.3    Spener, F.4    Köfeler, H.C.5    Thallinger, G.G.6
  • 28
    • 0024521543 scopus 로고
    • A concordance correlation coefficient to evaluate reproducibility
    • 1:STN:280:DyaL1M3kslKrtg%3D%3D 10.2307/2532051
    • Lin, L.: A concordance correlation coefficient to evaluate reproducibility. Biometrics 45, 255-268 (1989)
    • (1989) Biometrics , vol.45 , pp. 255-268
    • Lin, L.1
  • 29
    • 71549165598 scopus 로고    scopus 로고
    • Bi-Cross-Validation of the SVD and the nonnegative matrix factorization
    • Owen, A.B.; Perry, P.O.: Bi-Cross-Validation of the SVD and the nonnegative matrix factorization. Ann. Appl. Stat. 3, 564-594 (2009)
    • (2009) Ann. Appl. Stat. , vol.3 , pp. 564-594
    • Owen, A.B.1    Perry, P.O.2
  • 31
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: Open source software for rapid proteomics tools development
    • 1:CAS:528:DC%2BD1cXht12gtb3K 10.1093/bioinformatics/btn323
    • Kessner, D.; Chambers, M.; Burke, R.; Agusand, D.; Mallick, P.: ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008)
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agusand, D.4    Mallick, P.5
  • 32
    • 27644598142 scopus 로고    scopus 로고
    • Ambient mass spectrometry using desorption electrospray ionization (DESI): Instrumentation, mechanisms, and applications in forensics, chemistry, and biology
    • 1:CAS:528:DC%2BD2MXht1Sgu7nK 10.1002/jms.922
    • Takats, Z.; Wiseman, J.M.; Cooks, R.G.: Ambient mass spectrometry using desorption electrospray ionization (DESI): Instrumentation, mechanisms, and applications in forensics, chemistry, and biology. J. Mass Spectrom. 40, 1261-1275 (2005)
    • (2005) J. Mass Spectrom. , vol.40 , pp. 1261-1275
    • Takats, Z.1    Wiseman, J.M.2    Cooks, R.G.3
  • 33
    • 33845533193 scopus 로고    scopus 로고
    • Droplet dynamics and ionization mechanisms in desorption electrospray ionization mass spectrometry
    • 1:CAS:528:DC%2BD28XhtF2ntb%2FN 10.1021/ac0615807
    • Venter, A.; Sojka, P.E.; Cooks, R.G.: Droplet dynamics and ionization mechanisms in desorption electrospray ionization mass spectrometry. Anal. Chem. 78, 8549-8555 (2006)
    • (2006) Anal. Chem. , vol.78 , pp. 8549-8555
    • Venter, A.1    Sojka, P.E.2    Cooks, R.G.3
  • 36
    • 84863723868 scopus 로고    scopus 로고
    • Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging
    • Gerbig, S.; Golf, O.; Balog, J.; Denes, J.; Baranyai, Z.; Zarand, A.; Raso, E.; Timar, J.; Takats, Z.: Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging. Anal. Bioanal. Chem. 403, 2315-2325 (2012)
    • (2012) Anal. Bioanal. Chem. , vol.403 , pp. 2315-2325
    • Gerbig, S.1    Golf, O.2    Balog, J.3    Denes, J.4    Baranyai, Z.5    Zarand, A.6    Raso, E.7    Timar, J.8    Takats, Z.9
  • 37
    • 34247163207 scopus 로고    scopus 로고
    • Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
    • 105 10.1186/1471-2105-8-105
    • Kind, T.; Fiehn, O.: Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8, 105 (2007)
    • (2007) BMC Bioinformatics , vol.8
    • Kind, T.1    Fiehn, O.2
  • 38
    • 33646754900 scopus 로고    scopus 로고
    • Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm
    • 234 10.1186/1471-2105-7-234
    • Kind, T.; Fiehn, O.: Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 7, 234 (2006)
    • (2006) BMC Bioinformatics , vol.7
    • Kind, T.1    Fiehn, O.2
  • 39
    • 84903733662 scopus 로고    scopus 로고
    • Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry
    • 1:CAS:528:DC%2BC2cXpt1Kqurg%3D 10.1021/ac501075f
    • Strittmatter, N.; Rebec, M.; Jones, E.A.; Golf, O.; Abdolrasouli, A.; Balog, J.; Behrends, V.; Veselkov, K.A.; Takats, Z.: Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry. Anal. Chem. 86, 6555-6562 (2014)
    • (2014) Anal. Chem. , vol.86 , pp. 6555-6562
    • Strittmatter, N.1    Rebec, M.2    Jones, E.A.3    Golf, O.4    Abdolrasouli, A.5    Balog, J.6    Behrends, V.7    Veselkov, K.A.8    Takats, Z.9


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