Softwares from different companies

1- AB Sciex
a. BioAnalyst Software have fully integrated set of data processing tools for the identification and characterization of peptides and proteins using mass spectrometry data. b. MarkerView Software designed for metabolomics and protein/peptide biomarker profiling applications, allows to rapidly and easily review data to determine up- and down-regulation of endogenous compounds in complex samples. c. MRMPilot Software Trial version from https://licensing.absciex.com/download/index This streamlines the building and optimization of targeted peptide quantitative assays for biomarker verification or other targeted quantitative proteomic applications. a. ProteinPilot Software Trial version from https://licensing.absciex.com/download/index protein identification and quantitation, enabling to identify hundreds of peptide modifications and non-tryptic cleavages simultaneously; easily distinguish protein isoforms, protein subsets, and suppress false positives; and visualize peptide-protein associations and relationships a. ChemoView Software Trial version from https://licensing.absciex.com/download/index designed for data processing to quickly screen a series of compounds in a large set of FI/MS/MS data. The concentrations and equations of concentrations for all compounds are determined.

Softwares from different companies

2-Thermo Scientific
a. Mass Frontier 7.0 Spectral Interpretation Software: Mass Frontier provides the tools required to quickly transform mass spectral data into results. small molecule structural identification from MSn data with coverage on fragmentation mechanisms and client-server database capabilities for dynamic library searching and storage. It is applicable to a wide range of applications including metabolomics, forensics, natural products, impurities, and degradants research.
a. Xcalibur: It is a complete quantitative and qualitative analysis software package that enables you to acquire data specifically for analytes of interest, to perform confirmatory library searches, and to determine the concentration of analytes in samples.

Softwares from different companies

3- Bruker Daltonics
a. BioTools: It is designed for the interpretation of MS and MS/MS spectra of protein digests or peptides. b. WARP-LC: Accurate determination of LC-MS signal intensities, the correct detection of signal pairs or n-tuplets and the determination of quantitative ratios are the key responsibilities of WARP-LC. c. ClinProTools: Generation of classification models for Biomarker detection and evaluation d. The easy-to-use data post-processing software for visualization, data reduction, data mining and building predictive models from protein profiling data using Brukers MALDI-TOF mass spectrometers. e. MetaboliteTools: Dedicated software for the identification and confirmation of expected and known f. metabolites as well as the elucidation of unknowns. Predict and detect metabolites rapidly and evaluate small molecule differences between two samples. g. GenoTools: GenoTools represents a software solution for the analysis of genomics data generated by Bruker Daltonics MALDI-TOF mass spectrometers. h. Target Analysis: Based on high resolution and precise mass, in combination with True Isotopic Pattern, TargetAnalysis delivers a multi dimensional identification procedure for unambigous molecular formula identification in a sample such as drugs/metabolites in biological samples, food safety analysis, forensic toxicology or environmental testing.

Softwares from different companies

4- Agilent Technologies
a. GeneSpring GX: It provides powerful, accessible statistical tools for fast visualization and analysis of transcriptomics, genomics, proteomics and metabolomics data. b. MassHunter BioConfirm: It is ideally suited to support recombinant protein expression and process development, known-protein characterization, or synthetic peptide confirmation. c. MassHunter Metabolite ID: It vastly simplifies metabolite identification. Unique molecular feature extraction algorithms do a better job of finding metabolites. d. Mass Profiler Professional: It is the only chemometrics software package designed to exploit the high information content of mass spectrometry data. Provides comprehensive statistical tools including ANOVA, PCA, t-tests, volcano plots, hierarchical trees, SOMs, QT clustering, and SVMs for class prediction e. Spectrum Mill: It quickly identifies proteins and peptides via fast database searches, with automatic or manual match validation and unique algorithms that minimize false positives. It also offers de novo spectral interpretation for proteins not found in any database. Spectrum Mill software can identify relative abundance differences of twofold or greater without complicated isotope labeling.

Softwares from different companies

5- Waters
a. Quandepia: It is an extensible and searchable database for quantitative LC/MS and LC/MS/MS method information. Quanpedia simplifies and accelerates quantitative UPLC/MS/MS analytical method creation. b. Trendplot: It charts long-term system performance. Perform statistical analysis identify outliers within a sample run, or spot trends in historical data across many sample runs. c. TargetLynx: For high-throughput targeted quantification and confirmation analyses, complete with a full-range of automatic quality control checks. d. MassFragment: It is a chemically intelligent structure elucidation tool for the structural assignment of product ions of your known chemical structures. e. MetaboLynx XS: Rapidly detects the peaks in your LC/MS & LC/MS/MS sample analysis that result from in vitro or in vivo biotransformation. f. MarkerLynx: Processes complex multivariate data from LC/MS, LC/MS/MS, GC/MS, and GC/MS/MS metabonomic and metabolomic studies. g. BioPharmaLynx: Determines the identity, purity, and stability of biopharmaceutical products from peptide maps or intact proteins. h. ProteinLynx Global SERVER (PLGS): A mass-informatics platform for quantitative and qualitative proteomics research and the central analytical platform for Waters proteomics systems.

Databases that Aid in Protein Identification

1. SEQUEST: It is a proprietary tandem mass spectrometry data analysis program. SEQUEST, like many engines, identifies each tandem mass spectrum individually. The software evaluates protein sequences from a database to compute the list of peptides that could result from each. 2. Mascot: It is a proprietary identification program available from Matrix Science. It performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments rather than cross correlation. 3. PEAKS DB: It is a proprietary proteomic mass spectrometry database search engine, developed by Bioinformatics Solutions Inc. In addition to reporting database sequences, it also provides a list of sequences identified exclusively by de novo sequencing. The approach of considering de novo sequence results with those of database searching increases the efficiency of the search process, maintains speed and ultimately maintains a low false discovery rate.

Databases that Aid in Metabolite Identification

Human Metabolome Database www.hmdb.ca Functional Glycomics Gateway www.functionalglycomics.org MassBank www.massbank.jp Lipid Maps www.lipidmaps.org METLIN metlin.scripps.edu ExPASy-GlycoMod tool www.expasy.org/tools/glycomod Madison Metabolomic Consortium Database mmcd.nmrfam.wisc.edu HORA suite www.paternostrolab.org NIST Chemistry Web book webbook.nist.gov/chemistry CyberCell Database redpoll.pharmacy.ualberta.ca/CCDB Spectral Database for Organic Compounds riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi SpecInfo cds.dl.ac.uk/cds/datasets/spec/specinfo/specinfo.html

Software for Multivariate Statistical Analysis

XCMS https://xcmsonline.scripps.edu/ BioRad's KnowItAll Metabolomics Edition www.bio-rad.com Camo's The Unscrambler www.camo.com Umetrics' SIMCA-P www.umetrics.com High Resolution Spectroscopy (HiRes) mrs.cpmc.columbia.edu/hires.html BluGnome's BluFuse www.cambridgebluegnome.com R Project http://www.r-project.org/ Matlab http://www.mathworks.com/products/matlab/trial.html Minitab http://www.minitab.com/en-GB/products/minitab/free-trial Statistica http://www.statsoft.com/support/free-statistica-10trial/download/