ProteinProspector FAQ

Here is a list of questions asked about Protein Prospector. If you have any submissions/corrections please send them to Peter Baker at prbaker@itsa.ucsf.edu.

Licensing Issues

Questions About Using ProteinProspector

How do I get a licensed copy of ProteinProspector?

Send email to Marilyn Schwartz at mars@itsa.ucsf.edu and she will fax you a license agreement and order form for the software. The package runs on either the Windows NT or Sun UNIX platforms. If this fails then contact Peter Baker at prbaker@itsa.ucsf.edu.

Which computer platforms can I run a licensed copy of ProteinProspector on?

The package runs on either the Windows NT 3.51 and above (4.0 recommended) or Sun UNIX platforms 4.0.3 and above. There has been some talk about releasing an SGI version but this is not yet available.

Which web browser do I need to use?

Most web browsers should be OK with versions up to and including version 3.0.4 of ProteinProspector. The software was developed using Netscape so this is likely to work better.

The preferred browser for versions 3.1.x is Netscape 4.x. We have released a version of 3.1.1 which is back compatible with previous browsers and another version that works with Internet Explorer 4.

Versions 3.2.0 and above should work with any browser supporting JavaScript. Please contact us if you are having problems.

What are the main reasons why I would not want to run ProteinProspector on a local server?

1) You have to configure your computer as a web server.
2) You have to periodically download the databases from various sites on the web and run a program called FA-Index to make them usable by ProteinProspector.

What are the main reasons why I would want to run ProteinProspector on a local server?

1) Security concerns about web transmission of proprietary data.
2) Desire to search proprietary databases.
3) Desire for higher throughput searches with automated scripts.
4) Remoteness in the world leading to long internet transit times.
5) Better access to certain program features which require hard drive writing.

Now that PerSeptive Biosystems are distributing ProteinProspector will the web site be discontinued?

UCSF has no intention of discontinuing the web site, in fact all licensing is arranged to insist on allowing UCSF to retain that right. While you may be aware that PerSeptive Biosystems are distributing the ProteinProspector programs, UCSF will retain the right to distribute the programs directly to academic and nonprofit institutions. The programs will continue to contain capabilities which are essentially vendor independent.

How do I get MS-Fit to run with no Possible modifications?

It's different depending on your system, Mac, PC etc. On my PC if I hold down the control key and click then I can de-select any individual choice. Some variation of this like the shift key or the apple key should work on a Mac.

How do I get MS-Tag to work with ISD data?

One way of using MS-Tag is to subtract the mass of NH3 (17 Da) from each measured mass, which would give you a set of b ions rather than a set of c ions. You could generate a pseudo M+H by adding approx 1 Da to the last value (add OH + H and subtract NH3). You should use MS-Tag in No enzyme mode.

If the data contains both c and y ions you need to make sure that the "parent mass" you enter is consistent with both sets of ions. However if you can identify around 4-6 ions which are definitely of the same type then that should be enough to identify the protein. It doesn't matter if there's a gap of more than one amino acid between them.

Alternatively you could work out a partial amino acid sequence from the mass differences and use MS-Edman.

The above refers to releases previous to release 3.2.0. In 3.2.0 we added c-ions to the allowed fragment ion types.

Why is MS-Fit in version 3.1.1 slower than in previous versions?

Scoring was added in release 3.1.1. If you wish you can deselect scoring on the MS-Fit page.

Could you define the MS-Digest Index Number?

The index number actually represents the numerical location of the protein entry in the FASTA formatted sequence database file. i.e. index number 82367 is the 82367th protein in the file counting from the beginning of the file. We call it the MS-Digest index number because throughout the ProteinProspector package you can click on the number and be linked to the MS-Digest program for that protein. Note that with every revision of the database this number can change, however the accession numbers are constant. Hence, the index number itself is only meaningful for operations within the ProteinProspector programs.

Is there a reference for a paper that describes MS-Fit?

We don't yet have a paper out which deals with MS-Fit. If the reason for your request is that you are writing something and want to cite MS-Fit, the preference is that you do something like:

Baker, P.R. and Clauser, K.R. http://prospector.ucsf.edu.

Some people place it in the text, others in the reference list. It doesn't matter much to me, at the minimum giving the web URL in a methods section helps others the most. Please don't list anything in the URL after .ucsf.edu as that will change over time.

What should I be aware of when using the dbEST database?

1) Peptide mass fingerprinting in principle shouldn't typically be very effective with ESTs because you have digested a whole protein and EST's are only a few hundred basepairs, often on the order of 100-200. So you can only match a portion of your protein.

2) For the practical reason above the dbEST search feature was put into ProteinProspector mainly for searches using MS/MS spectra and sequence data; MS-Tag, MS-Edman.

3) Any searches you do with dbEST, SET THE PROTEIN MW RANGE TO ALL. dbEST is ~600 MB, the protein databases are ~100 MB, if you use a large MW range (default for example) then the preliminary MW sort takes a very long time.

4) When using the web server rather than ProteinProspector on the web, you are competing for CPU time against people all over the world. So for long dbEST searches it sometimes helps to break it into 2 searches. 1 with 3 frame translation, 1 with -3.

The -3 frame is only available in ProteinProspector release 3.1 and higher.

How do I change the timeout in Peer Web Services/Microsoft Internet Server?

1). First of all stop the www service.

2). From the Start Menu select Run and type in

This should start the Registry Editor.

3). In the registry editor select the directory

4). Highlight the parameter ScriptTimeout and select Modify from the edit menu. The decimal value is in seconds. The default is 15 minutes (900 seconds).

5). Exit the registry editor and restart the WWW service in the Internet Service Manager.