Literature DB >> 17121773

PrepMS: TOF MS data graphical preprocessing tool.

Yuliya V Karpievitch1, Elizabeth G Hill, Adam J Smolka, Jeffrey S Morris, Kevin R Coombes, Keith A Baggerly, Jonas S Almeida.   

Abstract

UNLABELLED: We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment. AVAILABILITY: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms

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Year:  2006        PMID： 17121773      PMCID： PMC2633108          DOI： 10.1093/bioinformatics/btl583

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

1.  Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry.

Authors:  Stefan Schaub; John Wilkins; Tracey Weiler; Kevin Sangster; David Rush; Peter Nickerson
Journal:  Kidney Int       Date:  2004-01       Impact factor: 10.612

2.  High-resolution serum proteomic features for ovarian cancer detection.

Authors:  T P Conrads; V A Fusaro; S Ross; D Johann; V Rajapakse; B A Hitt; S M Steinberg; E C Kohn; D A Fishman; G Whitely; J C Barrett; L A Liotta; E F Petricoin; T D Veenstra
Journal:  Endocr Relat Cancer       Date:  2004-06       Impact factor: 5.678

3.  Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins.

Authors:  John M Koomen; Lichen Nancy Shih; Kevin R Coombes; Donghui Li; Lian-chun Xiao; Isaiah J Fidler; James L Abbruzzese; Ryuji Kobayashi
Journal:  Clin Cancer Res       Date:  2005-02-01       Impact factor: 12.531

4.  Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques.

Authors:  Dariya I Malyarenko; William E Cooke; Bao-Ling Adam; Gunjan Malik; Haijian Chen; Eugene R Tracy; Michael W Trosset; Maciek Sasinowski; O John Semmes; Dennis M Manos
Journal:  Clin Chem       Date:  2004-11-18       Impact factor: 8.327

5.  Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.

Authors:  Jeffrey S Morris; Kevin R Coombes; John Koomen; Keith A Baggerly; Ryuji Kobayashi
Journal:  Bioinformatics       Date:  2005-01-26       Impact factor: 6.937

6.  Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform.

Authors:  Kevin R Coombes; Spiridon Tsavachidis; Jeffrey S Morris; Keith A Baggerly; Mien-Chie Hung; Henry M Kuerer
Journal:  Proteomics       Date:  2005-11       Impact factor: 3.984

7.  Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry.

Authors:  Timothy M Pawlik; Herbert Fritsche; Kevin R Coombes; Lianchun Xiao; Savitri Krishnamurthy; Kelly K Hunt; Lajos Pusztai; Jeng-Neng Chen; Charlotte H Clarke; Banu Arun; Mien-Chie Hung; Henry M Kuerer
Journal:  Breast Cancer Res Treat       Date:  2005-01       Impact factor: 4.872

8.  Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men.

Authors:  Bao-Ling Adam; Yinsheng Qu; John W Davis; Michael D Ward; Mary Ann Clements; Lisa H Cazares; O John Semmes; Paul F Schellhammer; Yutaka Yasui; Ziding Feng; George L Wright
Journal:  Cancer Res       Date:  2002-07-01       Impact factor: 12.701

9.  Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.

Authors:  Keith A Baggerly; Jeffrey S Morris; Kevin R Coombes
Journal:  Bioinformatics       Date:  2004-01-29       Impact factor: 6.937

10.  A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection.

Authors:  Yutaka Yasui; Margaret Pepe; Mary Lou Thompson; Bao-Ling Adam; George L Wright; Yinsheng Qu; John D Potter; Marcy Winget; Mark Thornquist; Ziding Feng
Journal:  Biostatistics       Date:  2003-07       Impact factor: 5.899
  10 in total
  14 in total

1.  Statistical contributions to proteomic research.

Authors:  Jeffrey S Morris; Keith A Baggerly; Howard B Gutstein; Kevin R Coombes
Journal:  Methods Mol Biol       Date:  2010

2.  Improved signal processing and normalization for biomarker protein detection in broad-mass-range TOF mass spectra from clinical samples.

Authors:  Maureen B Tracy; William E Cooke; Christine L Gatlin; Lisa H Cazares; Dennis M Weaver; O John Semmes; Eugene R Tracy; Dennis M Manos; Dariya I Malyarenko
Journal:  Proteomics Clin Appl       Date:  2011-07-13       Impact factor: 3.494

3.  Metabolomic analysis and visualization engine for LC-MS data.

Authors:  Eugene Melamud; Livia Vastag; Joshua D Rabinowitz
Journal:  Anal Chem       Date:  2010-11-04       Impact factor: 6.986

4.  Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles.

Authors:  Richard C Pelikan; Milos Hauskrecht
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

5.  A general-purpose baseline estimation algorithm for spectroscopic data.

Authors:  Donald A Barkauskas; David M Rocke
Journal:  Anal Chim Acta       Date:  2010-01-11       Impact factor: 6.558

6.  The knowledge-integrated network biomarkers discovery for major adverse cardiac events.

Authors:  Guangxu Jin; Xiaobo Zhou; Honghui Wang; Hong Zhao; Kemi Cui; Xiang-Sun Zhang; Luonan Chen; Stanley L Hazen; King Li; Stephen T C Wong
Journal:  J Proteome Res       Date:  2008-07-30       Impact factor: 4.466

7.  Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer.

Authors:  Monika Pietrowska; Lukasz Marczak; Joanna Polanska; Katarzyna Behrendt; Elzbieta Nowicka; Anna Walaszczyk; Aleksandra Chmura; Regina Deja; Maciej Stobiecki; Andrzej Polanski; Rafal Tarnawski; Piotr Widlak
Journal:  J Transl Med       Date:  2009-07-13       Impact factor: 5.531

Review 8.  Microproteomics: analysis of protein diversity in small samples.

Authors:  Howard B Gutstein; Jeffrey S Morris; Suresh P Annangudi; Jonathan V Sweedler
Journal:  Mass Spectrom Rev       Date:  2008 Jul-Aug       Impact factor: 10.946

9.  Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

Authors:  Chao Yang; Zengyou He; Weichuan Yu
Journal:  BMC Bioinformatics       Date:  2009-01-06       Impact factor: 3.169

10.  An introspective comparison of random forest-based classifiers for the analysis of cluster-correlated data by way of RF++.

Authors:  Yuliya V Karpievitch; Elizabeth G Hill; Anthony P Leclerc; Alan R Dabney; Jonas S Almeida
Journal:  PLoS One       Date:  2009-09-18       Impact factor: 3.240
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