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Definition of the "Isolation Width"?

Posted: Fri Jan 27, 2012 2:27 pm
Sorry for a rather simple, yet ambiguous question: When you enter a value prior to the data acquisition, is it the full-width or half-width. In other word, does a 2 Da isolation window mean "plus/minus 2 da around my precursor" or "plus/minus 1 da around my precursor".

I couldn't find the exact answer anywhere unfortunately.


Posted: Fri Jan 27, 2012 3:08 pm
by Craig
Hi Wen,

As far as I am aware, "isolation width" always refers to the full width. So a 2 Da isolation window means +/- 1 Da.


Posted: Sat Jan 28, 2012 7:59 am
by Infinity
I agree with Craig, -/+ 1Da centered at your precursor.

Posted: Sat Jan 28, 2012 8:46 am
I took a closer look at some data and both of you are right.

Mann published a paper about "100,000 peptide species" in a single HeLa run. They released two Lc-MS/MS with 2 and 16Da isolation respectively. If I took MS/MS from 2Da run and calculate dot-product to MS/MS in 16 Da within the same RT vicinity, the graph would offer an actual picture of what happened due the precursor isolation.

1-27-2012 9-35-16 PM.jpg



Posted: Sun Jan 29, 2012 8:11 pm
by karthikskamath
Yes Wen
As Craig n Infinity indicated it is +/- value. BTW could you please share this paper here? I am bit confused with another paper "Deep proteome and transcriptome mapping of a human cancer cell line". This figure really drives some interest. Thanks !!!


Posted: Mon Jan 30, 2012 8:04 am
The paper was published in JPR last year:
"More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS",

The conclusion of the paper is not surprising at all. It's consistent with our own observation based on the feature detected by Elucidator as well.

Posted: Mon Jan 30, 2012 10:52 pm
by karthikskamath
Hi Wen

Many thanks for sharing this paper.