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Programs:
Freeware and
shareware definitions
Site Title:
mMass - Open Source Mass Spectrometry Tool
Author(s):
Martin Strohalm, PhD.
Platform: PC
Site Origin: Institute of Chemical Technology,
Prague Department of Biochemistry and Microbiology
Address for download:
http://mmass.biographics.cz/
Program:
mMass presents an open source and multi-platform package of many tools
for mass spectrometric data analysis, mainly in proteomics.
(This program has yet to be reviewed by IonSource)
Site Title:
NCRR Proteomics Resource at PNNL (Software Tools)
Author(s):
NCRR
Platform: PC
Site Origin: NCRR
Address for download:
http://ncrr.pnl.gov/software/
Program:
Proteomics Software and Tools
Site Title: DBToolkit
Author(s):
Lennart
Martens
Platform: PC
Site Origin: Universiteit Gent
Address for download:
http://genesis.ugent.be/dbtoolkit/
Program:
DBToolkit
Reference: http://bioinformatics.oxfordjo
urnals.org/cgi/content/abstrac
t/21/17/3584
(article is free for download)
"DBToolkit is a user-friendly, easily extensible tool that
allows the processing of protein sequence databases to peptidecentric sequence
databases." (this is a quote from the paper)
Site Title: MassKinetics
Author(s):
L. Drahos and K. Vékey
Platform: PC
Site Origin: MassKinetics
Address for download:
http://www.chemres.hu/ms/masskinetics
Program:
MassKinetics 1.2 Light
Reference: L.
Drahos and K. Vékey, J. Mass Spectrom. 36, 237 (2001)
Theory and Windows-based program to calculate mass spectra. For research and
for teaching mass spectrometry and reaction kinetics.
Site Title: MS/MS Software,
Software Tools for Mass Spectrometry
Author(s):
Mike Senko
Platform: PC
Site Origin: MS/MS
Software
Address for download:
see links below
Program:
IsoPro
2.1: (freeware) "An old favorite, imagine having a periodic chart on
your PC that can perform mass calculations and isotopic simulations "
IsoPro
3.0 : (shareware/30days) $25/copy ($15 Academic). IUPAC values change as
more accurate mass measurements are made therefore a good calculator should be
user modifiable like this one is . go
to description
FragPro
1.0: (shareware/30days) $15/copy ($10 Academic) Unreviewed. go
to description
Site Title: WSEARCH SOFTWARE
Author(s):
Frank Antolasic
Platform: PC
Site Origin:
WSEARCH SOFTWARE www.wsearch.com.au
Address for download:
www.wsearch.com.au
Program: WSEARCH
"This is a Windows program that can read Multiple Mass spectral
file formats." Supports: Kratos DS90, AEI DS55, HP Chemstation, HP Pascal.(wow I thought I was the last one with a Pascal
workstation), Varian Saturn, Finnigan ITS40, Magnum, Shrader LRP files, JCAMP_DX
files, netCDF.
Site Title: Jim's Home Page
Author(s):
Jim Deline
Platform: Macintosh
Site Origin: http://home.pacbell.net/jdeline/
Address for download:
http://home.pacbell.net/jdeline/
Program: MFcalc(TM) elemental
composition calculator.
Site Title: Sherpa : "Your
Guide to the Peaks"
Author(s):
J. Alex Taylor
Platform: Macintosh
Site Origin: Home Page, http://www.hairyfatguy.com/Sherpa/
Address
for download:
http://www.hairyfatguy.com/Sherpa/download.html
Program: Sherpa
is "A Macintosh-based Expert System for LC/MS
& MS/MS Analysis" Sherpa contains a useful peptide calculator and
it is also useful for LC/MS analysis. "Sherpa Lite" is
available for free it will do theoretical protein digests but will not search a
sequence by mass.
Site Title: Bioanalytical Research Group, EMBL-Heidelberg
Author(s):
Matthias Mann
Platform: Macintosh
Site Origin: http://www.narrador.embl-heidelberg.de/GroupPages/Homepage.html
Address
for download:
Program: PeptideSearch.
Search a non-redundant protein database with a sequence tag, AA
sequence, and peptide mass data. The standalone program and database can
be downloaded from EMBL Protein and Peptide group. You will need to obtain a
password for use from Matthias Mann, but since Matthias left for the University
of Southern Denmark you might try the current group leader Matthias Wilm first
wilm@embl-heidelberg.de. The last update on the EMBL ftp server was Sept.
1997. This program and Matthias helped me out when I arrived at a company with
limited resources and no ms searchable database. Update: Peptide search is now a
module called
PepSea available as part of a software package offered for sale at
Protana. A current database can still be obtained at EMBL.
Site Title: MDL Information Systems
Author(s):
NA
Site Origin: http://www.mdli.com
Address for download:
http://www.mdli.com/cgi/dynamic/welcome.html
Programs:
Chime: (Macintosh PowerPC, PC
95,NT 4.0) 3D molecule viewer.
ISIS/Draw 2.2.1:(Macintosh PowerPC, PC Win95,
Win98,,NT 4.0)
Site Title: The GPM (The Global Proteome
Machine Organization)
Author(s):
Ron Beavis
Site Origin: http://www.thegpm.org/TANDEM/index.html
Address for download:
ftp://ftp.thegpm.org/
Programs: X!Tandem an open source
proteomics search engine for mass spectrometry data.
Site Title: MagTran (the magic transformer)
Author(s):
Zhongqi Zhang
Site Origin: Homepage
Address
for download:
http://www.geocities.com/SiliconValley/Hills/2679/magtran.html
Programs: MagTran, Freeware deconvolution
software for electrospray spectra. If you do not have the deconvolution
software package for your electrospray instrument, it is worth a try. Poster was presented at ASMS 1999.
Site Title: PC Software (NMR, IR, etc.)
Author(s):
Harold M. Bell
Site Origin: Virginia
Tech Chemistry Department
Address
for download:
http://www.chemistry.vt.edu/chem-dept/hbell/simulation/hb2/TESTPAGE.htm
Programs:
"APT simulates the attached proton test in
carbon-13 NMR."
"DECAY is a program that simulates radioactive decay."
"DEPT simulates the DEPT pulse sequence for distinguishing between
methine, methylene, and methyl carbons in carbon-13 NMR."
"FIDMAKER is a program that creates FIDs"
"FTNMR Simulator is a Microsoft Windows program that simulates the
prinicples and operation of Fourier Transform NMR."
"HETJ-2D simulates the two-dimensional heteronuclear J-spectroscopy
experiment."
"HOMOJ-2D simulates the two-dimensional homonuclear J-spectroscopy
experiment."
"IRREADER is a program that allows off-line
processing of FTIR datafiles (Perkin-Elmer, Galactic,
Nicolet, JCAMP)."
"NMRSM is a Microsoft Windows
version of a program for calculating spin-spin splitting patterns"
"VTFT is a program that performs Fourier transforms on FIDs."
"XHCORR simulates the two-dimensional carbon-proton correlation
experiment."
Disclaimer: We have no control over the content at these external
sites and claim no responsibility as to the integrity of the programs that they
supply. It is our suggestion that if you are performing a critical
function (as we all are) that you perform your own software validation before
proceeding. In addition we grant no licenses to use the software packages
supplied at these external sites and it is up to the end user to obtain the
grant of use. See disclaimer link below for further disclaimers of all warrantee.
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