Screen shot of the ProMass home page Introduction: Large biomolecules when ionized by electrospray (ESI) are predominantly multiply charged. When analyzed in the positive ion mode, peptides or proteins will be protonated at multiple sites as a result of the basic amino acids and amino terminus. On the other hand, oligonucleotides analyzed in the negative ion mode are de-protonated at multiple sites as a result of the acidic phosphate backbone. This multiple charging usually results in ESI mass spectra that contain a range of charge states. These complex spectra must be “deconvoluted” or “transformed” in order to order to determine the uncharged mass of the biomolecule. ProMass provides an automated platform for performing deconvolution of entire LC/MS data sets. Overview: ProMass is an automated biomolecule deconvolution and reporting software package that is used to process ESI/LC/MS data or single ESI mass spectra acquired on Thermo Scientific’s Xcalibur or Waters MassLynx data systems.
ProMass was designed from the start for high-throughput applications. In fact, the normal way to run ProMass is through the Xcalibur or MassLynx sample list. Therefore, you can run a list of samples and have ProMass process them at the end or batch reprocess the list at your convenience.
ProMass uses a novel deconvolution algorithm known as ZNova that produces artifact-free deconvoluted mass spectra. ZNova can be used to process data from a wide variety of biomolecules including proteins, oligonucleotides, peptides, etc. Unlike many other deconvolution algorithms, ZNova can accommodate low charge state spectra and data of low signal-to-noise ratio. ProMass reports the results automatically in an easy-to-use and interactive format viewable from any web browser.
A top-level summary page summarizes the results from multiple runs and displays them on a single hyperlinked page allowing you to navigate your results quickly. Target mass features allow you to search for multiple target masses from LC/MS data automatically. The target mass features include results color coding, allowing you to quickly hone in on the samples that may require further attention. ProMass HR includes additional features for high-resolution data processing by incorporating the full suite of algorithms from ProMass HR methods can utilize the PPL algorithms that allow for monoisotopic mass determination of isotopically resolved mass spectra or enhanced resolution of isotopically unresolved mass spectra. The PPL methods may be automated thru the same powerful mechanism as the standard version of ProMass. Results are displayed through the same easy-to-use and intuitive web-based output as well. Key Features of ProMass: ProMass is more than just deconvolution software.
ProMass is a tool that allows you to process and communicate your results in a highly collaborative web-based format. Automated deconvolution of biomolecule mass spectra to determine molecular mass: applicable to proteins, peptides, oligonucleotides, etc.
MassLynx Software is a fundamental platform for acquiring, analysing, managing and sharing mass spectrometry information. MassLynx provides intelligent control of an entire Waters mass spectrometry system, from the sample and solvent management components to the mass spectrometer and auxiliary detectors. MassLynx may acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The Sample List is a key feature of MassLynx, keeping everything about samples together in one place.
It is also the central place for initiating any activities relating to the sample. This 'sample-centric' approach simplifies the interaction with an LC/MS or GC/MS system, acquired data and processed results, increasing the speed at which sample data can be converted into valuable knowledge. MassLynx Software provides general purpose and specialised application managers dedicated to providing information for specific types of MS analyses and data:. QuanLynx, included as standard with MassLynx, for automated quantification. OpenLynx, also included as standard, for qualitative screening and identification. Targeted quantitative analysis, mass-directed purification, metabolite identification, deconvolution of complex chromatograms, metabonomics and metabolomics, protein identification and protein characterisation are available with optional application managers.
Mass Spectrometry Software Alphabetical by Program/Site Name Under Heading. New Links: Index Pages Software to design and simulate properties of instruments utilizing electric and magnetic fields to guide charged particles. EMBL Protein and Peptide Group archive of software for biological mass spectrometry. Index of peptide and protein software tools.
The hypertext version of the InfoMac software archive. Link is to the section of scientific software. Mostly commercial software with links to shareware resources. WWW Based Calculations Molecular Weight and Isotope Pattern Calculators Peptide/Protein Calculators, a probability based search engine for protein identification using peptide mass values or MS/MS data. Other Shareware and Freeware A limited amount of FTP space is available at this site for mass spectrometry shareware and freeware programs. Utilities to perform improved searches on HP Data Systems, maros for structural import on HP data systems, Programs for converting ASCII library files.
This is a shareware program that calculates isotopic ratio patterns for molecular fragments. Contains Java and JavaScript utilities for Mass Spectometry and peptide mapping. JCAMP-DX is a freeware program for interactive viewing of mass spectra. MASP is a freeware program predicting fragmentation-free mass spectra of libraries prepared by combinatorial synthesis. A simple freeware program for the calculation of molecular and formula weights and elemental compositions. Demo version of a molecular weight calculator program.
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Freeware molecular weight and percent composition calculator for Windows 95, 3.x, and DOS. A small Macintosh program that solves the equation: m/q = r2.B2/E.
A java applet that calculates all possible molecule masses on the basis the isotopes of the constituent atoms. IsoPro 3.0 for Windows '95 and NT as well as other shareware. A LabView VI library for working with HP chemstation files (LabView program required).
Oligo Analyzer is a freeware oligonucleotide analysis program which will calculate the molecular weight and the predicted melting temperature of your oligo and give the total number of each nucleotide. A computer analysis program for PCs, developed for the interpretation of oligopeptide MS/MS mass spectra, also suitable for fragments containing unnatural or modified amino acids. Home of PAWS, M/Z and other software.
SEQUEST is a Unix program that correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. Software for protein mass spectrometry including spectral analysis and protein identification. A Windows program that allows users to process 1-Dimensional FTICR files in native Bruker, Finnigan, IonSpec, and Midas formats. A Windows program for displaying HP Chemstation/Pascal, Kratos DS90/DS55, Finnigan ITS40, Magnum,Varian Saturn, Jcamp, Schrader and NetCDF file formats. Commercial Software Software design for acquisition or instrument control. ACD/SpecManager: MS module for spectroscopic processing and data management.
Software for mass spectrometry. Spectra database software from WILEY-VCH. Software for mass spectrometry and other analytical and training needs. Softbook interactive MS, GC, HPLC, and advanced GC training software. A program for mass spectral decomposition and peak identification. Utilities to perform improved searches on HP Data Systems, maros for structural import on HP data systems, Programs for converting ASCII library files.
Mass spectra and other spectral databases. Makers of Mass Frontier software for management and interpretation of mass spectra. Y2K and instrument control software for control of older GCMS systems such as PE, QMASS, Finnigan and HP. Mass spectrometer software upgrades for benchtop GCMS systems. Data acquisition and analysis for quadrupole mass spectrometers. A Windows based program for protein sequence and mass spectrometry analysis. Software for structure elucidation based on mass spectrometry.
MassSim is a mass spectrometer simulator intended for educational use and can import data from the NIST/EPA database. Mascot, a WWW tool for protein identification by matching mass spectrometry data againist protein and nucleic acid sequence databases. Company does a program called massim. The latest version, NIST 98, contains approximetely 130,000 evaluated electron ionization spectra of 108,000 compounds, nearly all with chemical structures. Makers of GC/MS data analysis software including The Wiley Registry of Mass Spectral Data. Y2K MS Data system upgrades and HP MS ChemStation enhancements.
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A Macintosh based expert system for LC/MS and MS/MS analysis. Mass spectrometry software for combinatorial chemistry and polymer analysis. The INEL home page for David Dahl's SIMION charged particle optics program.
Masslynx Download
Ready to run and custom software for mass spectrometry. Custom software development for laboratories utilizing high resolution mass spectrometry to measure dioxins/furans. © 1999, John Wiley & Sons, Ltd.
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