Question: Ways To Quantify Proteome Analysis Via Blast
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gravatar for James Smith
8.4 years ago by
James Smith150
James Smith150 wrote:

I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database. Usually multiple organisms are usually analyzed using this method and then the results are contrasted between each organism and relations are hypothesized.

However, to me, this seems like rather shallow data. I'd like to find a more quantifiable metric so that I can say that there is a good relation between the query and hit proteins. I've gone to quantify the number of hydrophilic residues in each protein since it's an important metric in my database. However I'm having a difficult time scoring these results using the e-value from blast and this count.

Can anyone refer me to similar papers which have done this or suggest methods of further analysis?

proteomics protein scoring blast • 2.0k views
ADD COMMENTlink written 8.4 years ago by James Smith150

Why do you want to do this with BLAST? There is dedicated software.

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k

Michael, I am not sure what kind of software you mean. Assuming he really has protein sequences and not protein identifiers BLAST (tblastn) might be a good way to annotate the sequences. On the other hand many proteomics approaches indeed already give identifiers, in which case runningBLAST doesn't make sense.

ADD REPLYlink written 8.4 years ago by Chris Evelo10.0k

True if he indeed has protein sequences. However, proteomics is mostly done with MS methods that give peptide sequences and not whole proteins. Inferring protein quantities from those alone is mostly guesswork IMO.

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k

I'm using a "complete proteome" from embl-ebi. Eg: http://www.ebi.ac.uk/integr8/FtpSearch.do;jsessionid=CBD21F2A85C32065DD7A40EA1823B4AE?orgProteomeId=137

ADD REPLYlink modified 21 days ago by RamRS24k • written 8.4 years ago by James Smith150
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