Spectrometry
There are many formats for mass spectrometry data. The Proteome Commons Project http://www.proteomecommons.org provides a library of functions for reading many of the widely used formats. By using the MATLAB-Java interface you can leverage the functions in the Proteome Commons IO library to allow...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (40): Accessing Mass spectrometry data using the Proteome Commons IO Library Download |
msInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file.
You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and...
Platforms: Windows
License: Freeware | Download (389): msInspect Download |
MassCalculator is a Perl module that implements common mass computations in mass spectrometry. SYNOPSIS use InSilicoSpectro::InSilico::MassCalculator; InSilicoSpectro::InSilico::MassCalculator::init(insilicodef.xml); MassCalculator Perl library is intended to support common mass...
Platforms: *nix
License: Freeware | Size: 1.4 MB | Download (90): InSilicoSpectro::InSilico::MassCalculator Download |
MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry. SYNOPSIS MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence...
Platforms: *nix
License: Freeware | Size: 16.38 KB | Download (92): MassSpec::CUtilities Download |
OpenChrom is a handy tool specially designed to help you with chromatography. It is based on the Eclipse Rich Client Platform (RCP).
Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual...
Platforms: Windows
License: Freeware | Download (475): OpenChrom Download |
A viewer for chromatography and mass spectrometry data in the AIA standard formats. AIA is the industry standard for chromatography data interchange, and in turn is based on the netCDF data format and libraries.
Until now, if you wanted to work with a chromatogram on a Mac, you needed to export...
Platforms: Mac
License: Freeware | Size: 3.5 MB | Download (55): Xhromatogram for Mac OS Download |
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS)
peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/).
iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or...
Platforms: Windows, Mac, Linux
License: Freeware | Size: 1.48 MB | Download (44): iPiG Download |
JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 922.33 KB | Download (50): JPhysChem modeling tool Download |
JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 17.88 KB | Download (49): JRasterCreator Download |
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 1.59 MB | Download (44): Manuelito Download |
Spectre for mass spectrometry. (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data. (working on mzDATA). Provides filters, alignment- and export tools.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 3.62 MB | Download (49): MS-Spectre: quantitative LC-MS analysis Download |
MZ-Analyzer is a tool for visualization and analysing of multiple mass spectrometry data in 2D and 3D mode, including the function of quantitating the LC-peak of the specified identified peptides.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 252.07 KB | Download (46): MZ-Analyzer Download |
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 89.09 MB | Download (52): MZmine 2 Download |
Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
Platforms: Windows, Mac, Linux
License: Freeware | Size: 2.43 MB | Download (50): protein-ms Download |
PRIDE Converter converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS). The...
Platforms: Mac
License: Freeware | Size: 15.14 MB | Download (45): PRIDE Converter Download |
The Open Mass Spectrometry Search Algorithm [OMSSA] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical...
Platforms: Mac
License: Freeware | Size: 22.1 MB | Download (43): OMSSA Parser Download |
massXpert is about mass spectrometry. This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system. With massXpert you actually have four programs in one : 1. With the XpertDef module you define brand new polymer chemistries (what are the...
Platforms: Mac
License: Freeware | Size: 15.87 MB | Download (40): massXpert Download |
Visualize chromatographic properties for peptides from replicate, multi-site HPLC-MRM Mass Spectrometry experiments. RT Viewer was developed to easily visualize and troubleshoot chromatographic properties of a study across multiple laboratories.
Platforms: *nix
License: Freeware | Size: 1.46 MB | Download (38): RTViewer Download |
mMass presents open source multi-platform package of tools for precise mass spectrometric data analysis and interpretation. It is written in Python language and released under GNU General Public License, so it's portable to different computer platforms and has a good potential to be easily...
Platforms: Mac
License: Freeware | Size: 32 MB | Download (437): mMass for Mac Download |
Mascot Distiller uses a unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists. This core functionality can be extended by adding one or more toolboxes.
These are optional collections of tools for specific...
Platforms: Windows, Windows Vista, 7
License: Freeware | Download (433): Mascot Distiller Download |