Program Functionality Reviews

and how to....s

IonSource Reviews

Proteomic and MS Programs

Program Reviews

New 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.

Scaffold ^® - An updated (Jan 2007) review of the basic functions of the comparative proteomic program Scaffold ^®. The basic premise behind Scaffold ^® is that when you combine the results from multiple search engines you increase proteomic coverage. Beyond combining results, Scaffold ^® provides a statistical analysis of the imported data and provides a GUI that does a very good job of comparing multiple runs side by side. Scaffold also comes bundled with X!Tandem (a sequence search engine) that can utilize up to four processors.

T2X - We describe, step by step, how to convert Xcalibur ^® .raw files to the new generic file format mzXML. T2x is a free program from the Institute of Systems Biology. The tutorial then shows you how to view your data with a free viewer from Insilicos. We also demonstrate how the data can be searched with Phenyx, one of the few search engines that can accept mzXML data. We would like to remind you to support the common file format mzXML! Tell your MS vendor to support mzXML, if enough of us do, they will. Recently theGPM announced that their sequence search engine can now accept mzXML data
(t2x is in semi retirement, the program below, ReAdW, was made to handle Xcalibur 1.4 files.).

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 (done)
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 http://www.jdl.ac.cn/user/yfu/pfind/index.html
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 webmaster@ionsource.com directly.

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