I think Sequest is around $10,000 and currently runs only on NT4; Mascot
runs on a variety of OS's. They were willing to tailor one for us to run
on a Linux PC for the price of $5000 per CPU, which we run internally using
standard FASTA formatted databases. To match the speed of Mascot, you need
to use "turbo-sequest", which for fast runs requires the production of an
indexed database that can take maybe an hour to make for a non-redundant
protein database. So for example, you might make an indexed database for
tryptic peptides where cysteines are carbamidomethylated; however, you'd
need a different index for pyridylethylated cysteine. Mascot doesn't
require an index for each type of digest or cysteine alkylation, yet
nevertheless seems to run as fast as turbosequest. Also, we have been able
to add any sort of modification that we like.
Rich Johnson (Immunex, Seattle, WA)
"MSweeney"
<mattsweeney@eart To: Recipients of ABRF List <abrf@aecom.yu.edu>
hlink.net> cc:
Sent by: Subject: Re: SEQUEST vs. MASCOT
Association of
Biomolecular
Resource
Facilities
<abrf-request@aec
om.yu.edu>
01/18/2001 01:29
PM
SEQUEST
You can control your own libraries that are searched (create your own).
You do the searches privately on your own box.
You can script up fancy things with cgi-bin/perl.
You can can play with post trans mods a bit better.
Mascot
0n the web it is free.
It is hella fast.
You send the search results and dtas over the great unknowns of the web.
Private???NO.
You can get a local version as well.
You must use the provided libs on the web.
I guess you can cgi/perl stuff here too.
Matt Sweeney
mattsweeney@earthlink.net
Mass Spec Consulting
Training/Operations/Consulting/Method Development
LC/MS Pharmacokinetics, Peptides, Proteins, Metabolism,
Maintenance Classes, Specialist in Finnigan Equipment and Software
-----Original Message-----
From: Dave Russel <daverussel@hotmail.com>
To: Recipients of ABRF List <abrf@aecom.yu.edu>
Date: Thursday, January 18, 2001 6:15 AM
>Dear all,
>
>I have some experience with LC-MS but just started to do peptide analysis.
>
>I noticed two software packages "Sequest" and "Mascot". Can anyone tell me
>the similarities or differences (pro's and con's) of both systems.
>
>Did I eventually miss other interesting software packages worthwile
>considering?
>
>thank you very much in advance
>best regards
>
>Dave
>_________________________________________________________________________
>Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.
>
>
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