From: Matthew C. <mat...@gm...> - 2012-08-31 22:14:45
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Hi Corey, Actually it's the opposite. The Waters RAW viewer would show calibrated masses, the pwiz-based ones would not. The Waters API exports uncalibrated masses and pwiz doesn't know how to do anything with the lock-mass channel yet. Sorry, -Matt On 8/31/2012 4:39 PM, Broeckling,Corey wrote: > I tried using the command line version as well, and it did not work. I am beginning to suspect that > MSconvert is trying to use my lockmass channel (function 3) to correct my MS and DDA masses, but I > have already done so. Is there a way to turn this off? > > Corey > > *From:*Broeckling,Corey > *Sent:* Friday, August 31, 2012 12:16 PM > *To:* 'su...@pr...' > *Subject:* MSconvert / seeMS question > > I have used MSconvert to convert a waters Raw file to mzXML format. I used the latest 32 bit > version, as the 64 bit version was crashing for me. I was visually comparing the data in raw Waters > format vs the seeMS viewed mzXML file, and the masses viewed in the spectrum are different than the > raw data. Oddly enough, the base peak ,/z listed in the table at the bottom of the seeMS viewer > lists the base peak with the correct accurate mass, but the spectrum displays it shifted by about > 0.05 Da. (the base peak mass for spectrum 1 in waters is listed as 113.9627, it is listed in the > seeMS spectrum as 114.04, and is listed in the tabular area at the bottom as 113.96266; I also > opened it in inSilicos viewer, and in that window, the BP on the chromatogram is labeled as 113.963, > while in the spectrum view it is labeled as 114.039). > > I am confused as to why the labels are different, and want to make sure that my data is intact > following conversion. Any advice is appreciated. > > Corey |