Mass spectrometry and bioinformatics analysis data

Proteome analysis of Cryptosporidium parvum and C. hominis using two-dimentional electrophoresis, image analysis and tandem mass spectrometry

Until recently, Cryptosporidium was thought to be a single species genus. Molecular studies now showthat there are at least 10 valid species of this parasite. Among them, two morphologically identical species, C.hominis and C. parvum are the most pathogenic identified to date and share 97% of identical genomes.Post-genomic analyses is therefore necessary to explore further the...

Bioinformatics methods and applications for functional analysis of mass spectrometry based proteomics data

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

SUMMARY New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating pe...

Census 2: isobaric labeling data analysis

MOTIVATION We introduce Census 2, an update of a mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an op...

MALDIquant: a versatile R package for the analysis of mass spectrometry data

UNLABELLED MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as sp...

Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert

UNLABELLED With the ever-increasing demand for biopolymer mass spectrometry, specialized software is needed to both predict and process mass spectrometric data. With massXpert, we present a proteomics-oriented program mainly concerned with protein physico-chemistry and protein/peptide mass spectra simulations. AVAILABILITY The massXpert program is free for academic and commercial use at http:...