Literature DB >> 15691857

SpecAlign--processing and alignment of mass spectra datasets.

Jason W H Wong1, Gerard Cagney, Hugh M Cartwright.   

Abstract

SUMMARY: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra; one set was acquired prior to instrument calibration and the other following calibration. AVAILABILITY: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.

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Year:  2005        PMID： 15691857     DOI： 10.1093/bioinformatics/bti300

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


  43 in total

1.  Precision enhancement of MALDI-TOF MS using high resolution peak detection and label-free alignment.

Authors:  Maureen B Tracy; Haijian Chen; Dennis M Weaver; Dariya I Malyarenko; Maciek Sasinowski; Lisa H Cazares; Richard R Drake; O John Semmes; Eugene R Tracy; William E Cooke
Journal:  Proteomics       Date:  2008-04       Impact factor: 3.984

2.  Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data.

Authors:  Alejandro Cruz-Marcelo; Rudy Guerra; Marina Vannucci; Yiting Li; Ching C Lau; Tsz-Kwong Man
Journal:  Bioinformatics       Date:  2008-08-11       Impact factor: 6.937

3.  Identifying differences in protein expression levels by spectral counting and feature selection.

Authors:  P C Carvalho; J Hewel; V C Barbosa; J R Yates
Journal:  Genet Mol Res       Date:  2008-04-15

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.  Mesoporous silica chips for selective enrichment and stabilization of low molecular weight proteome.

Authors:  Ali Bouamrani; Ye Hu; Ennio Tasciotti; Li Li; Ciro Chiappini; Xuewu Liu; Mauro Ferrari
Journal:  Proteomics       Date:  2010-02       Impact factor: 3.984

6.  Tailoring of the nanotexture of mesoporous silica films and their functionalized derivatives for selectively harvesting low molecular weight protein.

Authors:  Ye Hu; Ali Bouamrani; Ennio Tasciotti; Li Li; Xuewu Liu; Mauro Ferrari
Journal:  ACS Nano       Date:  2010-01-26       Impact factor: 15.881

7.  Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome.

Authors:  Ralph Kissen; Per Winge; Diem Hong Thi Tran; Tommy S Jørstad; Trond R Størseth; Tone Christensen; Atle M Bones
Journal:  BMC Genomics       Date:  2010-03-22       Impact factor: 3.969

8.  A novel preprocessing method using Hilbert Huang Transform for MALDI-TOF and SELDI-TOF mass spectrometry data.

Authors:  Li-Ching Wu; Hsin-Hao Chen; Jorng-Tzong Horng; Chen Lin; Norden E Huang; Yu-Che Cheng; Kuang-Fu Cheng
Journal:  PLoS One       Date:  2010-08-31       Impact factor: 3.240

9.  Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet.

Authors:  Nha Nguyen; Heng Huang; Soontorn Oraintara; An Vo
Journal:  Bioinformatics       Date:  2010-09-15       Impact factor: 6.937

10.  Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease.

Authors:  Christopher C L Liao; Nicholas Ward; Simon Marsh; Tan Arulampalam; John D Norton
Journal:  BMC Cancer       Date:  2010-08-06       Impact factor: 4.430
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