[BiO BB] Mascot parameters

[Mike Marchywka]

Would anyone be willing to post a link to a tutorial or give us a quick 
explanation
of the issues  involved in precise protein identification and 
quantification?

I'm interested in a practical problems in immunology where you read about 
results like
this:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16463039&query_hl=3&itool=pubmed_docsum
"Immunization with oxidized ovarian tumor cell lines may represent an 
improved therapeutic strategy to stimulate a polyclonal anti-tumor cellular 
immune response and hence extend remission in ovarian cancer."


and have to ask, " if you wanted to prepare a pure, highly immunogenic 
antigen, should you
make it with clean side chains or should you oxidize or otherwise modify 
some of them?"
If you were a dendritic cell looking for the results of a neutrophil attack, 
you may suspect
that the HOCl or H2O2  modified proteins are good candidates for being from 
pathogens.
Some drugs that seem to produce autoimmune reactions seem to do so by 
covalently
modifiying host proteins- you really have to suspect that small amounts of 
unusual
proteins could be very interesting.

If you design a dendritic cell vaccine using a single defined antigen
you may reasonably  speculate that observed immune response could be due to 
modified
versions ("impurities" ) of the intended antigen. How hard would it be to 
find
out what is actually in your  "pure antigen" ? ( presumably you would then 
attempt
to make something which consists primarily of each impurity and test it
for immunogenicity)

I've always wondered what the limitations are for identifcation and 
measurement of
these things.

Thanks.







>From: "Fabio Cerqueira" <frcerqueira at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] Mascot parameters
>Date: Mon, 12 Feb 2007 13:30:21 +0100
>
>Hi,
>
>Does anybody there use Mascot for protein identification by MS/MS ion 
>serch?
>I'm trying to use it for the first time, but I don't know how options to
>check in
>the fixed and variable modifications.
>
>Concerning the fixed modifications I'd like to indicate a C-term mass of
>14.01570; and for the amino acids C, D, E  the masses: 160.03068,
>129.04264, and 143.05829, respectively.
>
>Concerning the variable modifications, I'd like to indicate 
>phosphorylation,
>oxidation of methionine and loss of water in amino acids S and T.
>Phosphorylation and oxidation of methionine are easy. But I don't know
>how option to choose concerning the loss of water in S and T.
>
>Could anybody help me?
>
>Thanks, Fabio.
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
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