Data pre-processing in liquid chromatography-mass spectrometry-based proteomics

被引：57
|
作者：
Zhang, XA [1 ]
Asara, JM
Adamec, J
Ouzzani, M
Elmagarmid, AK
机构：
[1] Purdue Univ, Bindley Biosci Ctr, W Lafayette, IN 47907 USA
[2] Purdue Univ, Dept Comp Sci, W Lafayette, IN 47907 USA
[3] Beth Israel Deaconess Med Ctr, Boston, MA 02215 USA
来源：
BIOINFORMATICS | 2005年 / 21卷 / 21期
关键词：
D O I：
10.1093/bioinformatics/bti660
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Motivation: In a liquid chromatography-mass spectrometry (LC-MS)-based expressional proteomics, multiple samples from different groups are analyzed in parallel. It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance. Results: We have developed an algorithm for spectrum deconvolution. A two-step alignment algorithm is proposed for recognizing peaks generated by the same peptide but detected in different samples. The quality of LC-MS data is evaluated using statistical tests and alignment quality tests.
引用
收藏
页码：4054 / 4059
页数：6
相关论文
共 50 条
  • [1] Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics
    Xie, Fang
    Liu, Tao
    Qian, Wei-Jun
    Petyuk, Vladislav A.
    Smith, Richard D.
    JOURNAL OF BIOLOGICAL CHEMISTRY, 2011, 286 (29) : 25443 - 25449
  • [2] LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY-BASED PROTEOMICS OF NITROSOMONAS
    Wessels, Hans J. C. T.
    Gloerich, Jolein
    van der Biezen, Erwin
    Jetten, Mike S. M.
    Kartal, Boran
    METHODS IN ENZYMOLOGY: RESEARCH ON NITRIFICATION AND RELATED PROCESSES, VOL 486, PART A, 2011, 486 : 465 - 482
  • [3] An objective comparison of pre-processing methods for enhancement of liquid chromatography-mass spectrometry data
    Fredriksson, Mattias
    Petersson, Patrik
    Magnus, Joerten-Karlsson
    Axelsson, Bengt-Olof
    Bylund, Dan
    JOURNAL OF CHROMATOGRAPHY A, 2007, 1172 (02) : 135 - 150
  • [4] Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics
    Kim, Yeoun Jin
    Feild, Brian
    FitzHugh, William
    Heidbrink, Jenny L.
    Duff, James W.
    Heil, Jeremy
    Ruben, Steven M.
    He, Tao
    ANALYTICAL BIOCHEMISTRY, 2009, 393 (02) : 155 - 162
  • [5] Non-labeling liquid chromatography-mass spectrometry-based quantitative proteomics
    Li, X.
    Yi, E.
    Zhang, H.
    Aebersold, R.
    MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (08) : S324 - S324
  • [6] Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications
    Qian, Wei-Jun
    Jacobs, Jon M.
    Liu, Tao
    Camp, David G., II
    Smith, Richard D.
    MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (10) : 1727 - 1744
  • [7] MSroi: A pre-processing tool for mass spectrometry-based studies
    Perez-Cova, Miriam
    Bedia, Carmen
    Stoll, Dwight R.
    Tauler, Roma
    Jaumot, Joaquim
    CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 2021, 215
  • [8] Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data
    Bylund, D
    Danielsson, R
    Malmquist, G
    Markides, KE
    JOURNAL OF CHROMATOGRAPHY A, 2002, 961 (02) : 237 - 244
  • [9] A liquid chromatography-mass spectrometry-based metabolome database for tomato
    Moco, Sofia
    Bino, Raoul J.
    Vorst, Oscar
    Verhoeven, Harrie A.
    de Groot, Joost
    van Beek, Teris A.
    Vervoort, Jacques
    de Vos, C. H. Ric
    PLANT PHYSIOLOGY, 2006, 141 (04) : 1205 - 1218
  • [10] LIQUID CHROMATOGRAPHY MASS SPECTROMETRY-BASED PROTEOMICS: BIOLOGICAL AND TECHNOLOGICAL ASPECTS
    Karpievitch, Yuliya V.
    Polpitiya, Ashoka D.
    Anderson, Gordon A.
    Smith, Richard D.
    Dabney, Alan R.
    ANNALS OF APPLIED STATISTICS, 2010, 4 (04): : 1797 - 1823
12345