Literature DB >> 18442284

A computational strategy to analyze label-free temporal bottom-up proteomics data.

Xiuxia Du1, Stephen J Callister, Nathan P Manes, Joshua N Adkins, Roxana A Alexandridis, Xiaohua Zeng, Jung Hyeob Roh, William E Smith, Timothy J Donohue, Samuel Kaplan, Richard D Smith, Mary S Lipton.   

Abstract

Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still remain related to how best to extract biological information from dynamic proteomics data, for example, challenges related to extraneous variability, missing abundance values, and the identification of significant temporal patterns. This paper describes a strategy that addresses these issues and demonstrates its values for analyzing temporal bottom-up proteomics data using data from a Rhodobacter sphaeroides 2.4.1 time-course study.

Entities:  

Mesh：

Substances：

Year:  2008        PMID： 18442284      PMCID： PMC2574618          DOI： 10.1021/pr0704837

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  26 in total

1.  An accurate mass tag strategy for quantitative and high-throughput proteome measurements.

Authors:  Richard D Smith; Gordon A Anderson; Mary S Lipton; Ljiljana Pasa-Tolic; Yufeng Shen; Thomas P Conrads; Timothy D Veenstra; Harold R Udseth
Journal:  Proteomics       Date:  2002-05       Impact factor: 3.984

2.  Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling.

Authors:  T P Conrads; K Alving; T D Veenstra; M E Belov; G A Anderson; D J Anderson; M S Lipton; L Pasa-Tolić; H R Udseth; W B Chrisler; B D Thrall; R D Smith
Journal:  Anal Chem       Date:  2001-05-01       Impact factor: 6.986

3.  Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.

Authors:  Mary S Lipton; Ljiljana Pasa-Tolic'; Gordon A Anderson; David J Anderson; Deanna L Auberry; John R Battista; Michael J Daly; Jim Fredrickson; Kim K Hixson; Heather Kostandarithes; Christophe Masselon; Lye Meng Markillie; Ronald J Moore; Margaret F Romine; Yufeng Shen; Eric Stritmatter; Nikola Tolic'; Harold R Udseth; Amudhan Venkateswaran; Kwong-Kwok Wong; Rui Zhao; Richard D Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-12       Impact factor: 11.205

4.  A Bayesian missing value estimation method for gene expression profile data.

Authors:  Shigeyuki Oba; Masa-aki Sato; Ichiro Takemasa; Morito Monden; Ken-ichi Matsubara; Shin Ishii
Journal:  Bioinformatics       Date:  2003-11-01       Impact factor: 6.937

5.  LSimpute: accurate estimation of missing values in microarray data with least squares methods.

Authors:  Trond Hellem Bø; Bjarte Dysvik; Inge Jonassen
Journal:  Nucleic Acids Res       Date:  2004-02-20       Impact factor: 16.971

6.  Quantitative proteomics by stable isotope labeling and mass spectrometry.

Authors:  Sheng Pan; Ruedi Aebersold
Journal:  Methods Mol Biol       Date:  2007

Review 7.  Advances in proteomics data analysis and display using an accurate mass and time tag approach.

Authors:  Jennifer S D Zimmer; Matthew E Monroe; Wei-Jun Qian; Richard D Smith
Journal:  Mass Spectrom Rev       Date:  2006 May-Jun       Impact factor: 10.946

8.  PRISM: a data management system for high-throughput proteomics.

Authors:  Gary R Kiebel; Ken J Auberry; Navdeep Jaitly; David A Clark; Matthew E Monroe; Elena S Peterson; Nikola Tolić; Gordon A Anderson; Richard D Smith
Journal:  Proteomics       Date:  2006-03       Impact factor: 3.984

9.  Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach.

Authors:  Wei-Jun Qian; Matthew E Monroe; Tao Liu; Jon M Jacobs; Gordon A Anderson; Yufeng Shen; Ronald J Moore; David J Anderson; Rui Zhang; Steve E Calvano; Stephen F Lowry; Wenzhong Xiao; Lyle L Moldawer; Ronald W Davis; Ronald G Tompkins; David G Camp; Richard D Smith
Journal:  Mol Cell Proteomics       Date:  2005-03-07       Impact factor: 5.911

10.  Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry.

Authors:  Eric F Strittmatter; Lars J Kangas; Konstantinos Petritis; Heather M Mottaz; Gordon A Anderson; Yufeng Shen; Jon M Jacobs; David G Camp; Richard D Smith
Journal:  J Proteome Res       Date:  2004 Jul-Aug       Impact factor: 4.466
View more
  14 in total

1.  A glimpse into the proteome of phototrophic bacterium Rhodobacter capsulatus.

Authors:  Ozlem Onder; Semra Aygun-Sunar; Nur Selamoglu; Fevzi Daldal
Journal:  Adv Exp Med Biol       Date:  2010       Impact factor: 2.622

Review 2.  Proteomics: a pragmatic perspective.

Authors:  Parag Mallick; Bernhard Kuster
Journal:  Nat Biotechnol       Date:  2010-07-09       Impact factor: 54.908

3.  System estimation from metabolic time-series data.

Authors:  Gautam Goel; I-Chun Chou; Eberhard O Voit
Journal:  Bioinformatics       Date:  2008-09-04       Impact factor: 6.937

4.  Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes.

Authors:  Ronghu Wu; Noah Dephoure; Wilhelm Haas; Edward L Huttlin; Bo Zhai; Mathew E Sowa; Steven P Gygi
Journal:  Mol Cell Proteomics       Date:  2011-05-07       Impact factor: 5.911

Review 5.  A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

Authors:  Melissa M Matzke; Joseph N Brown; Marina A Gritsenko; Thomas O Metz; Joel G Pounds; Karin D Rodland; Anil K Shukla; Richard D Smith; Katrina M Waters; Jason E McDermott; Bobbie-Jo Webb-Robertson
Journal:  Proteomics       Date:  2012-11-08       Impact factor: 3.984

6.  Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry.

Authors:  Johanna M Smeekens; Weixuan Chen; Ronghu Wu
Journal:  J Am Soc Mass Spectrom       Date:  2014-11-26       Impact factor: 3.109

7.  Mass spectrometric analysis of the N-glycoproteome in statin-treated liver cells with two lectin-independent chemical enrichment methods.

Authors:  Haopeng Xiao; Ju Eun Hwang; Ronghu Wu
Journal:  Int J Mass Spectrom       Date:  2017-05-27       Impact factor: 1.986

8.  Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-Fourier transform mass spectrometry.

Authors:  Prahlad K Rao; G Marcela Rodriguez; Issar Smith; Qingbo Li
Journal:  Anal Chem       Date:  2008-08-09       Impact factor: 6.986

Review 9.  Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Authors:  I-Chun Chou; Eberhard O Voit
Journal:  Math Biosci       Date:  2009-03-25       Impact factor: 2.144

10.  A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS).

Authors:  Weixuan Chen; Johanna M Smeekens; Ronghu Wu
Journal:  Mol Cell Proteomics       Date:  2014-04-01       Impact factor: 5.911
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.