Program Functionality Reviews

and how to....s

IonSource Reviews 

Proteomic and MS Programs


Program Reviews
New Proteome Cluster from Bioproximity, a fee-for-service on-line protein database MS search engine
New  MassQC   MassQC uses a battery of metrics to evaluate a standard protein digest. MassQC brings quality to proteomics.  This program evaluates your mass spectrometers system suitability. MassQC lets you know how well your system is performing giving you the information you need to proceed with a simple or complex proteomic experiment. Start with a free demo copy of MassQC, which is fully functional for 30 days.  The demo version has all of the functionality of the licensed version.
OMSSA -Learn how to download, install, and use OMSSA a free protein database MS search engine. In addition, learn to search mass spectrometry data with OMSSA.  This was an easy install.
Phenyx - This is a review of the MS based, sequence database search engine, Phenyx from Geneva Bioinformatics (GeneBio) S.A.  Specifically, this is a review of the freely available web version of Phenyx.  Phenyx is also available as a fully functional local version. The web version is very powerful, only limited by an inability to upload custom databases, and limited by the number of data files that can be up loaded at any one time.  Currently the web version of Phenyx allows the simultaneous upload of four data files per session. 
  ReAdW is an updated version of t2x.  ReAdW is able to convert ThermoFinnigan, Xcalibur 1.4, MS .raw files to mzXML, whereas t2x could not. ReAdW is also backwards compatible with Xcalibur 1.3.  The program works just about the same as t2x, except that now you need to specify whether the data is centroid or profile. The conversion to mzXML seems to be a lot faster with ReAdW.
CompassXport - Is a free program from Bruker that will convert Bruker and some Agilent MS datafiles to the new mzXML universal MS file format. Support mzXML.


Tell us what free MS program you would want us to review and also show you how to install and use.  Just enter the name of the program and the preferred operating system.  There is no personal information required just enter the name of the program that you would like to have detailed in the box below and press the button.

Here is an example submission, "X!Tandem on Windows 2000"

Here are the votes so far 

MSight 1 vote (high on our list, free from ExPASy, 3D mapping and differential proteomics!)
Phenyx 5 votes (
Analyst QS 5 votes (ABI commercial program, we will try to get it.)
CompassXport 1.1 2 votes  (done)
OMSSA on Windows XP 6 votes  (open access and free, high on our list) (done)
DTASelect on Windows XP 3 votes  (requires an MTA with Scripps, need to be an edu to get it for free, we will see)
Sequest 3 vote (Thermo Electron, commercial program, we will try to get it.)
Mascot 1 vote (Matrix Science, commercial program, we will try to get it.)
pfind 2 vote
2d ms 1 vote (Can't find this tool)
ProteinLynx globalserver 1 vote
x!tandem 1 vote
TransProteomic Pipeline (GUI) 1 vote
Protein Prospector on Windows XP 1 vote
Using the GPMDB on a local machinez 1 vote
LCQ Tune 1 vote

Priority will be given to programs that are freely available because they are available to a wider audience and they are easier for us to get our hands on.  If a vendor is interested in having their program reviewed please contact directly.





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Last updated:  Tuesday, January 19, 2016 02:51:41 PM
























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