NBIC Proteomics Tools

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Package Category Domain Description Author/contact Publication Software
2Dwarp mass spectrometry proteomics A Two-Dimensional Method for Time Aligning Liquid Chromatography Mass Spectrometry Data. The algorithm called 2Dwarp correct the time shift occurring in LC-MS chromatograms. Modifications in the COW algorithm have been made using overlapping peak area of 3 dimensional Gaussian which size were obtained from extracted peaks of the reference and sample chromatogram. The software is to be used by data analysts working on LC-MS data. Frank Suits

and Peter Horatovitch

paper

pubmed:21349866

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2Dwarp - Taverna Workflow mass spectrometry proteomics A Two-Dimensional Method for Time Aligning Liquid Chromatography Mass Spectrometry Data. The algorithm called 2Dwarp correct the time shift occurring in LC-MS chromatograms. Modifications in the COW algorithm have been made using overlapping peak area of 3 dimensional Gaussian which size were obtained from extracted peaks of the reference and sample chromatogram. The software is to be used by data analysts working on LC-MS data. Frank Suits

and Peter Horatovitch

paper

pubmed:21349866

download
BMRF protein function, prediction proteomics BMRF is an easy to use R program for protein function prediction using Markov Random Field analysis. Inferences are made by Markov Chain Monte Carlo. Besides function prediction this method estimates accurately the network parameters. Yiannis Kourmpetis

and Cajo ter Braak

pubmed:20195360

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LysNDeNovo peptide identication proteomics LysNDeNovo analyses ETD spectra which utilizes the presence of a single fragment ion series to assign the peptide sequence. Our de novo sequencing approach results in a significant higher number of peptides identified than searching a dataset with other methods. Moreover, the de novo results allow the determination of point mutations as well as conserved regions between proteins of different species. Bas van Breukelen

pubmed:20077410

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MASDA mass spectrometry proteomics R-package for Mass Spectrometry Data Analysis, The package includes routines for loading mass spectrometry data from CSV files, doing baseline correction and normalization, peak detection and filtering, peak clustering across spectra, peak filtering and some visualization of results Wouter Meuleman

and Lodewyk Wessels

paper

pubmed:18257918

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StatQuant toolbox proteomics A post quantification analysis toolbox for improving quantitative mass spectrometry Bas van Breukelen

pubmed:19336442

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