Brett
Chris Turck at UCSF and I use a variation of this to perform ZoomScan Walking on
nano-spray of tryptic digests for protein ID. We can get well over 300 MS/MS scans in a
single file. Then we send this file to SEQUEST.
see our ASMS 2000 poster at
http://home.earthlink.net/~mattsweeney/820.html
Cap temp of 150. Std ESI tune. Long Max inject times (1000ms or more) for the MS/MS mode
(saved in the tune). I did this on an older software version that lets you do parent ion
mapping. You get to choose the full scan window that it looks at for ms/ms candidate ions
(we chose 7amu) and then 10 amu for the zoomscan step. This lets you get good coverage of
the ions in the range of interest and allows you to look at the zoom-scan in a wider
window. This is important because of the random distribution of masses across the mass
range. Sometimes the largest ion in the 7 amu full scan window is only a weak intensity
heavy isotope of an ion in the next 7 amu window over. By making the zoomscan window
wider we can later go back and note this. The MS/MS parent mass will be chosen from the
full scan 7 amu window. I think we take the 2 or three largest in the 7 amu window.
That's it. Get ready for BIG files. We often cherry pick the spectra for Dbase searching
rather than dumping the whole file.
Matt Sweeney
mattsweeney@earthlink.net
Mass Spec Consulting
Training/Operations/Consulting/Method Development
LC/MS Pharmacokinetics, Peptides, Proteins, Metabolism,
Maintenance Classes, Specialist in Finnigan Equipment and Software
-----Original Message-----
From: Brett Phinney <phinney1@msu.edu>
To: Recipients of ABRF List <abrf@aecom.yu.edu>
Date: Friday, August 11, 2000 10:42 AM
Subject: LCQ Deca ion Mapping
>I'm planning to do some experiments with the Deca for determining
>phosphorylation sites. The ion mapping methods look promising. Has anyone
>tried mapping phosphorylation sites using the ion mapping function in the
>Deca? Are there any optimization steps that are particularly useful?
>
>On a related note, We currently have the Newojective Picoview set up as the
>source, and I think the ion mapping methods require static infusion. How do
>other people do infusion with this source?
>
>
>Thanks a lot
>
>Brett
>
>
>
>-------------------------------------
>Brett Phinney, Ph D.
>Department of Biochemistry
>Mass Spectrometry Facility
>Michigan State University
>Phone 517-353-6767
>
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