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MALDIViz
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Facilitates visualization, statistical analysis, and high-quality image and data export. MALDIViz is a comprehensive informatics application for MALDI HTS data. This package provides a theme on top of Shiny, allowing the creation of visually attractive dashboards. It also offers user selectable options for generating a 3D PCA plot, for classification and identification of major sources of variation in the data.
MetPP / METabolomics Profiling Pipeline
Analyzes metabolomics data generated from the 2D gas chromatography time-of-flight mass spectrometry (GCxGC-TOF MS) instrument. MetPP is able to recognize the concentration difference of the spiked-in metabolite standards between sample groups. It is composed of different modules for: retention index matching, peak filtering and merging, peak list alignment, quant mass conversion, normalization, statistical significance tests and pattern recognition.
PEAKS
Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed and accuracy of the database search. Each protein obtains a score by adding its three highest peptide CAA scores, and the protein feature of a peptide is the maximum score of the proteins containing this peptide. PEAKS also provides a user-friendly interface to show each resultant peptide spectrum match from de novo sequencing.
hEIDI / (h) Exploitation et Integration des Donnees d'Identification
Manages and combines both identifications and semiquantitative data related to multiple liquid chromatography-mass spectrometry (LC−MS)/MS analyses. hEIDI can be used to compile analyses and retrieve lists of nonredundant protein groups. It allows direct comparison of series of analyses, on the basis of protein groups, while ensuring consistent protein inference and also computing spectral counts. The tool was able to compare pools of analyses in projects for which up to 1500 search results had been combined.
SpecOMS / Spectra Open Modification Search
Handles the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database. It contains SpecXtract, which computes the number of common (or shared) fragment masses for any pair of spectra, SpecTrees, a data structure to store all the input spectra without any filtering, and SpecFit to analyse the pairs provided by SpecXtract.
Mass-Up
A software tool for the analysis of MALDI data. This is an application that covers the whole process of MALDI data analysis, from data preprocessing to complex data analyses. Mass-Up incorporates the most common analyses, aside from protein identification and focusing in biomarker discovery, such as statistical tests-based biomarker discovery, clustering, PCA, and classification. In addition, other less common analyses such as quality control and biclustering are also included. Therefore, Mass-Up provides users with a wide range of tools to analyze and explore their MALDI data.
MultiAlign
Aligns multiple liquid chromatography-mass spectrometry (LC-MS) datasets to one another by clustering mass and chromatographic elution features across datasets. The MultiAlign application provides advanced visualization and manipulation capabilities for LC-MS datasets acquired on high resolution mass spectrometers. Functionalities include overlaid 2D plots, alignment plots, normalizations, and basic statistical comparisons. MultiAlign uses the LCMSWARP algorithm to align LC-MS datasets to a master list (mass tag database or a single LC-MS dataset) and then consolidate features into a consensus map. These features can be matched to an accurate mass and time (AMT) tag database to identify the LC-MS features.
pkDACLASS
Provides a complete data analysis solution for the users of MALDI-TOF MS proteomics raw data especially biomedical researchers with no statistics background. pkDACLASS classifies the samples based on the peaks using the randomForest R package classifier in addition to considering equal numbers of cases and controls for the classification process. It offers flexibility to the users to accomplish the complete and integrated analysis in one step or conduct analysis as a flexible platform and reveal the results at each and every step of the analysis.
Open-pFind
New
Allows users to investigate databases. Open-pFind consists of a two-steps search algorithm that first preprocesses mass-spectrometry (MS) data, and calibrates and extracts multiple precursor ions corresponding to each tandem mass spectrum. Secondly, the MS/MS data is searched against the indexed database. It can be used for key factors that affect the identification rate, including unexpected modifications, amino acid mutations, semi-/non-specific digestion and co-eluting peptides.
MassHunter Workstation Software
Provides intuitive, yet powerful, instrument control, data acquisition, qualitative and quantitative data analysis, and reporting for Agilent time-of-flight (TOF), quadrupole time-of-flight (Q-TOF), ICP-MS, and triple quadrupole systems. Designed from the ground up to make MS analyses easier from tuning to final report MassHunter Workstation software can be complemented by application-specific MassHunter software packages that provide even more power and stream-lined operation for specialized analytical tasks such as expression profiling.
Proteome Discoverer
Obsolete
A package for protein identification and quantification in biologic complex samples. It covers a wide range of possible proteomic analyses from proteins and peptides identification to post-translational modification. It searches in many databases (SEQUEST, Z-Core, Mascot, …) and several dissociation technics (CID, HCD, ETD) for complete analyses. Proteome Discover automatizes data analyse and allows to easily represent results thanks to modules like GO enrichment.
Firmiana
Obsolete
Allows scientists to deposit mass spectrometry (MS) raw files, perform proteome identification and quantification online, carry out bioinformatics analyses, and extract knowledge. Firmiana offers a way to easy visualize results without the need for programming expertise. It aims to facilitate for users the entire process of bioinformatics analysis from raw MS data to generate biological knowledge. The tool permits to automate large-scale data processing by using streamlined data computing workflows.
STEM / STrategic Extractor for Mascot's results
Obsolete
Processes large-scale mass spectrometry-based proteomics data. STEM is a stand-alone computational tool that evaluates, integrates, and compares large datasets produced by Mascot. STEM is compatible with quantitative proteomics studies that utilize various stable isotope tags. This software is designed to execute high-speed processing/organization of experimental data from a large-scale proteomics study. The STEM V-mode removes unreliable candidates from the large amount of Mascot search data, removes redundant peptide assignments for individual proteins, and efficiently extracts and integrates valuable information relevant to peptide/protein identification. The STEM C-mode compares lists of identified proteins, and proteins found in common between the lists and/or unique to a list from a specific analysis can be pulled out rapidly, enabling easy comparison of very complex proteomics results.
Visualize
Obsolete
Provides a comprehensive proteomics data analysis method. Visualize is a workstation application with an intuitive graphical user interface (GUI). It brings together different approaches to examine complex proteomics data sets at both the low level of Mass Spectrometry (MS) spectra and the identification details as well as the high levels of quantitation, analysis, and annotation to produce the output and figures required to communicate the results in presentations, publications, and applications.
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