Blog and Searching 'Perfect' Data

[Simon Chiang]

ProteomeCommons now has a community blog: http://proteomecommons.org/blog/browse.jsp
The blog is in beta but works for the most part. I'm going to post
something about my experiments in searching Mascot with perfect
predicted data.

To do so I released a new module ms-uniprot. At present it has only
one task, 'entry', which pulls down a UniProt entry as fasta, xml, etc
using an accession number. For example:

% gem install ms-uniprot
% rap uniprot/entry P02768 --: dump

I also updated ms-mascot for the post. Here are the commands to
predict and fragment tryptic peptides 3-residues or longer.

% gem install ms-uniprot ms-mascot
% tap run — uniprot/entry P02768 –: digest --min-length 3 --:i
mascot/fragment --:s mascot/format_mgf --: dump P02768.mgf

And now to submit the spectra to Mascot.

% tap run -- mascot/submit P02768.mgf --params:USEREMAIL
your....@email.edu --: dump

NOTE: I update ms-mascot to use tap-mechanize and the latest version
of tap. In the latest version the dump/load tasks have changed
slightly, so heads up.

[Simon Chiang]

[Simon Chiang]

No idea why that posted twice... anyhow I just put a blog post up
regarding searching Mascot with 'perfect' data.

http://proteomecommons.org/blog/?i=102&e=2

[Simon Chiang]