Chromatography Forum

Afternoon.

I am trying to deconvolute LC-MS data of nucleic acid digest of large fragments. Since the monoistopic mass is not present at these mass ranges I am trying to determine the average mass weighted from the distribution.

Xcaliber doesn't smooth enough to turn a distribution into a single peak from Orbitrap FTMS data.

The Xcaliber roadmap has a file converted which in a single step goes from .raw to .cdf which can be read by Bruker's DataAnalysis. I know DataAnalysis has the smoothing and averaging capabilities that I require. However when I load the chromatogram, a single scan has multiple lines that look like a distribution for a single isotope of a real distribution. It seems that I'm stuck in line spectra and the "profile" button is grayed out. If I go into options and switch to "profile" spectra only and still nothing.

I've tried to find some third party options, OpenChrom loads the chromatogram as a weird amount of peaks. I can't find other software that handles the .raw.

Any suggestions?

Hi Johte

I've no experience with large molecules, but our lab uses msconvert (from Proteowizard) to convert Thermo .raw files to .mzxml which can then be read by any number of free MS tools like xcms... that might be helpful?

Helen

File-conversion is really problematic for high-resolution data. Most software packages are at least not able to handle HR data.

Did you observed difference when profile or centroid mode was used for the acquired data?

Why you don’t use the additional software packages provided by Thermo, e.g.
http://www.thermoscientific.com/en/prod ... tware.html

Some of these packages are really cheap, for example Tox-ID.

File-conversion is really problematic for high-resolution data. Most software packages are at least not able to handle HR data.

Did you observed difference when profile or centroid mode was used for the acquired data?

Why you don’t use the additional software packages provided by Thermo, e.g.
http://www.thermoscientific.com/en/prod ... tware.html

Some of these packages are really cheap, for example Tox-ID.

We have Xtract but I'm working in negative mode and my sales rep has confirmed that it's only for positive. You know, I could do deconvolution by hand but you can't even smooth your distribution into an average mass. It also seems on default the program assigns the mass to the apex of an isotope to which you have to switch to "sticks" to get the centroid. Xcalibur is extremely limiting and doesn't provide a lot of the basic options that many other vendors provide for their instruments. Bruker's DataAnalysis is leaps and bounds better.

You can convert a .raw to a .cdf within the roadmap but DataAnalysis doesn't handle the file very well.