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 option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features. AVAILABILITY AND IMPLEMENTATION: Census 2 supports multiple input file formats including MS1/MS2, DTASelect, mzXML and pepXML. It requires JAVA version 6 or later to run. Free download of Census 2 for academic users is available at http://fields.scripps.edu/census/index.php. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (approximately 250%) and unique peptides (approximately 30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively. AVAILABILITY: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Abstract Summary: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). We describe how YADA enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data. Availability: http://fields.scripps.edu/yada Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.