메뉴 건너뛰기




Volumn 15, Issue 7, 2016, Pages 2198-2210

LaCyTools: A Targeted Liquid Chromatography-Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides

Author keywords

alpha 1 antitrypsin; bioinformatics; glycoproteomics; immunoglobulin G; liquid chromatography; mass spectrometry; profiling; quality control; relative quantitation

Indexed keywords

GLYCOPEPTIDE;

EID: 84977090983     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.6b00171     Document Type: Article
Times cited : (101)

References (33)
  • 1
    • 33748195979 scopus 로고    scopus 로고
    • Glycosylation in cellular mechanisms of health and disease
    • Ohtsubo, K.; Marth, J. D. Glycosylation in cellular mechanisms of health and disease Cell 2006, 126, 855-867 10.1016/j.cell.2006.08.019
    • (2006) Cell , vol.126 , pp. 855-867
    • Ohtsubo, K.1    Marth, J.D.2
  • 4
    • 84867774199 scopus 로고    scopus 로고
    • Glycan profiles of the 27 N-glycosylation sites of the HIV envelope protein CN54gp140
    • Pabst, M.; Chang, M.; Stadlmann, J.; Altmann, F. Glycan profiles of the 27 N-glycosylation sites of the HIV envelope protein CN54gp140 Biol. Chem. 2012, 393, 719-730 10.1515/hsz-2012-0148
    • (2012) Biol. Chem. , vol.393 , pp. 719-730
    • Pabst, M.1    Chang, M.2    Stadlmann, J.3    Altmann, F.4
  • 5
    • 0034625468 scopus 로고    scopus 로고
    • Structural models for carcinoembryonic antigen and its complex with the single-chain Fv antibody molecule MFE23
    • Boehm, M. K.; Perkins, S. J. Structural models for carcinoembryonic antigen and its complex with the single-chain Fv antibody molecule MFE23 FEBS Lett. 2000, 475, 11-16 10.1016/S0014-5793(00)01612-4
    • (2000) FEBS Lett. , vol.475 , pp. 11-16
    • Boehm, M.K.1    Perkins, S.J.2
  • 6
    • 33645100367 scopus 로고    scopus 로고
    • Comprehensive glyco-proteomic analysis of human α1-antitrypsin and its charge isoforms
    • Kolarich, D.; Weber, A.; Turecek, P. L.; Schwarz, H.-P.; Altmann, F. Comprehensive glyco-proteomic analysis of human α1-antitrypsin and its charge isoforms Proteomics 2006, 6, 3369-3380 10.1002/pmic.200500751
    • (2006) Proteomics , vol.6 , pp. 3369-3380
    • Kolarich, D.1    Weber, A.2    Turecek, P.L.3    Schwarz, H.-P.4    Altmann, F.5
  • 9
    • 84862238705 scopus 로고    scopus 로고
    • Determination of site-specific glycan heterogeneity on glycoproteins
    • Kolarich, D.; Jensen, P. H.; Altmann, F.; Packer, N. H. Determination of site-specific glycan heterogeneity on glycoproteins Nat. Protoc. 2012, 7, 1285-1298 10.1038/nprot.2012.062
    • (2012) Nat. Protoc. , vol.7 , pp. 1285-1298
    • Kolarich, D.1    Jensen, P.H.2    Altmann, F.3    Packer, N.H.4
  • 11
    • 45549094069 scopus 로고    scopus 로고
    • GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans
    • Ceroni, A.; Maass, K.; Geyer, H.; Geyer, R.; Dell, A.; Haslam, S. M. GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans J. Proteome Res. 2008, 7, 1650-1659 10.1021/pr7008252
    • (2008) J. Proteome Res. , vol.7 , pp. 1650-1659
    • Ceroni, A.1    Maass, K.2    Geyer, H.3    Geyer, R.4    Dell, A.5    Haslam, S.M.6
  • 14
    • 84879968670 scopus 로고    scopus 로고
    • Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry
    • Yu, C.-Y.; Mayampurath, A.; Hu, Y.; Zhou, S.; Mechref, Y.; Tang, H. Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry Bioinformatics 2013, 29, 1706-1707 10.1093/bioinformatics/btt190
    • (2013) Bioinformatics , vol.29 , pp. 1706-1707
    • Yu, C.-Y.1    Mayampurath, A.2    Hu, Y.3    Zhou, S.4    Mechref, Y.5    Tang, H.6
  • 15
    • 77952980825 scopus 로고    scopus 로고
    • MMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data
    • Strohalm, M.; Kavan, D.; Novák, P.; Volný, M.; Havlíček, V. mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data Anal. Chem. 2010, 82, 4648-4651 10.1021/ac100818g
    • (2010) Anal. Chem. , vol.82 , pp. 4648-4651
    • Strohalm, M.1    Kavan, D.2    Novák, P.3    Volný, M.4    Havlíček, V.5
  • 16
    • 77954772536 scopus 로고    scopus 로고
    • MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
    • Pluskal, T.; Castillo, S.; Villar-Briones, A.; Oresic, M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data BMC Bioinf. 2010, 11, 395 10.1186/1471-2105-11-395
    • (2010) BMC Bioinf. , vol.11 , pp. 395
    • Pluskal, T.1    Castillo, S.2    Villar-Briones, A.3    Oresic, M.4
  • 17
    • 71449097951 scopus 로고    scopus 로고
    • Alignment of capillary electrophoresis-mass spectrometry datasets using accurate mass information
    • Nevedomskaya, E.; Derks, R.; Deelder, A. M.; Mayboroda, O. A.; Palmblad, M. Alignment of capillary electrophoresis-mass spectrometry datasets using accurate mass information Anal. Bioanal. Chem. 2009, 395, 2527-2533 10.1007/s00216-009-3166-1
    • (2009) Anal. Bioanal. Chem. , vol.395 , pp. 2527-2533
    • Nevedomskaya, E.1    Derks, R.2    Deelder, A.M.3    Mayboroda, O.A.4    Palmblad, M.5
  • 18
    • 84941057683 scopus 로고    scopus 로고
    • Glycoforms of Immunoglobulin G Based Biopharmaceuticals Are Differentially Cleaved by Trypsin Due to the Glycoform Influence on Higher-Order Structure
    • Falck, D.; Jansen, B. C.; Plomp, R.; Reusch, D.; Haberger, M.; Wuhrer, M. Glycoforms of Immunoglobulin G Based Biopharmaceuticals Are Differentially Cleaved by Trypsin Due to the Glycoform Influence on Higher-Order Structure J. Proteome Res. 2015, 14, 4019-4028 10.1021/acs.jproteome.5b00573
    • (2015) J. Proteome Res. , vol.14 , pp. 4019-4028
    • Falck, D.1    Jansen, B.C.2    Plomp, R.3    Reusch, D.4    Haberger, M.5    Wuhrer, M.6
  • 22
    • 84949036097 scopus 로고    scopus 로고
    • MassyTools: A high throughput targeted data processing tool for relative quantitation and quality control developed for glycomic and glycoproteomic MALDI-MS
    • Jansen, B. C.; Reiding, K. R.; Bondt, A.; Hipgrave Ederveen, A. L.; Palmblad, M.; Falck, D.; Wuhrer, M. MassyTools: A high throughput targeted data processing tool for relative quantitation and quality control developed for glycomic and glycoproteomic MALDI-MS J. Proteome Res. 2015, 14, 5088-5098 10.1021/acs.jproteome.5b00658
    • (2015) J. Proteome Res. , vol.14 , pp. 5088-5098
    • Jansen, B.C.1    Reiding, K.R.2    Bondt, A.3    Hipgrave Ederveen, A.L.4    Palmblad, M.5    Falck, D.6    Wuhrer, M.7
  • 23
    • 79952595565 scopus 로고    scopus 로고
    • The NumPy Array: A Structure for Efficient Numerical Computation
    • van der Walt, S.; Colbert, S. C.; Varoquaux, G. The NumPy Array: A Structure for Efficient Numerical Computation Comput. Sci. Eng. 2011, 13, 22-30 10.1109/MCSE.2011.37
    • (2011) Comput. Sci. Eng. , vol.13 , pp. 22-30
    • Van Der Walt, S.1    Colbert, S.C.2    Varoquaux, G.3
  • 24
    • 34247500374 scopus 로고    scopus 로고
    • Python for Scientific Computing
    • Oliphant, T. E. Python for Scientific Computing Comput. Sci. Eng. 2007, 9, 10-20 10.1109/MCSE.2007.58
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 10-20
    • Oliphant, T.E.1
  • 25
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D Graphics Environment
    • Hunter, J. D. Matplotlib: A 2D Graphics Environment Comput. Sci. Eng. 2007, 9, 90-95 10.1109/MCSE.2007.55
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 90-95
    • Hunter, J.D.1
  • 26
    • 84966282998 scopus 로고
    • Centrum voor Wiskunde en Informatica: Amsterdam, Technical Report CS-R9526.
    • Van Rossum, G.; Drake, Jr., F. L. Python Reference Manual; Centrum voor Wiskunde en Informatica: Amsterdam, 1995; Technical Report CS-R9526.
    • (1995) Python Reference Manual
    • Van Rossum, G.1    Drake, F.L.2
  • 27
    • 84977110105 scopus 로고    scopus 로고
    • (accessed January 7, 2014).
    • Anaconda, 2016. https://store.continuum.io/cshop/anaconda/ (accessed January 7, 2014).
    • (2016) Anaconda
  • 28
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: Open source software for rapid proteomics tools development
    • Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. ProteoWizard: open source software for rapid proteomics tools development Bioinformatics 2008, 24, 2534-2536 10.1093/bioinformatics/btn323
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 29
    • 77949961607 scopus 로고    scopus 로고
    • Why Modern CPUs Are Starving and What Can Be Done about It
    • Alted, F. Why Modern CPUs Are Starving and What Can Be Done about It Comput. Sci. Eng. 2010, 12, 68-71 10.1109/MCSE.2010.51
    • (2010) Comput. Sci. Eng. , vol.12 , pp. 68-71
    • Alted, F.1
  • 31
    • 84925535007 scopus 로고    scopus 로고
    • The HDF Group. (accessed December 2015).
    • The HDF Group. Hierarchical Data Format, version 5, 1997. http://www.hdfgroup.org/HDF5 (accessed December 2015).
    • (1997) Hierarchical Data Format, Version 5
  • 32
    • 34548671166 scopus 로고    scopus 로고
    • Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction
    • Palmblad, M.; Mills, D. J.; Bindschedler, L. V.; Cramer, R. Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction J. Am. Soc. Mass Spectrom. 2007, 18, 1835-1843 10.1016/j.jasms.2007.07.018
    • (2007) J. Am. Soc. Mass Spectrom. , vol.18 , pp. 1835-1843
    • Palmblad, M.1    Mills, D.J.2    Bindschedler, L.V.3    Cramer, R.4
  • 33
    • 80051997026 scopus 로고
    • Robust Tests for the Equality of Variances
    • Brown, M. B.; Forsythe, A. B. Robust Tests for the Equality of Variances J. Am. Stat. Assoc. 1974, 69, 364-367 10.1080/01621459.1974.10482955
    • (1974) J. Am. Stat. Assoc. , vol.69 , pp. 364-367
    • Brown, M.B.1    Forsythe, A.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.