RE: FW: Corra questions?
Mi-Youn Brusniak
I replied directly to your email but the delivery failed (see below).
Again, I tried to answer you data acquisition method of exclusion for Corra
analysis.
Please find your question and answer below.
I hope you get this message by corra group.
Mi-Youn
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Subject: RE: FW: Corra questions?
Date: Mon, 6 Jun 2011 12:00:50 -0700
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Dear Dayle,
It's dependent on how you "ignore masses". More specifically, if you use set
of "exclusion MS1 peptide ions" and acquired sufficient MS1 profiled dataset
for lower abundant peptide ions (increasing MS1 scan time such as two MS2
scan per one MS1 scan ratio), Corra works fine. On the other hands, if you
just let vendor software to exclude peptide ions that are already shipped to
MS2 fragmentation on the fly dynamically, the quantification calculated by
Corra might not be reliable.
Cheers,
Mi-Youn
Mi-Youn Brusniak, PhD
Computational Biologist/Sr. Software Engineer
p 206.732.1327
Institute for Systems Biology | Seattle Proteome Center | 401 Terry Ave N.
Seattle WA 98109
Revolutionizing science. Enhancing life.
-----Original Message-----
From: DS [mailto:ihbipro...@hotmail.com]
Sent: Monday, June 06, 2011 12:05 AM
To: Mi-Youn Brusniak
Subject: Re: FW: Corra questions?
Hi Mi-Youn,
Currently our MS method will ignore masses that have already had
fragment spectra acquired. Primarily to increase the hits on low
abundant peptides in the tail of more high abundant peptides. I'm
assuming for application within Corra this may not be a good idea.
What is your perspective?
Best wishes,
Dayle.