Using Genome database in InsPecT

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karthikskamath
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Using Genome database in InsPecT

Postby karthikskamath » Tue Jul 02, 2013 5:28 pm

I want to use genome database (assembled genome with no annotation) on InsPecT search engine for identifying proteins from my mass spec runs. Did some one in the forum use the similar combination? If so, is it possible to perform search using genome on InSpecT? If not are there any other dedicated software for this kind of work (I have already tried Mascot and six frame translated database)?

Craig
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Postby Craig » Tue Jul 02, 2013 8:46 pm

I'm not that familiar with InsPecT, so I'm not sure if you can directly search a genome database. However, as a workaround you can just do the six-frame translation yourself so you can search a proteome database. EMBOSS Sixpack looks like it could do this even for a large genome.

Kelstrup
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Postby Kelstrup » Tue Jan 28, 2014 6:00 am

I guess you would benefit (almost need) high mass accuracy if you are working with a very large search space. As far as I know, Inspect does not support this.


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