offline 2D-LC-MS data view

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sll022003@gmail.com
Posts: 3
Joined: May 21st, 2019, 1:48 pm

offline 2D-LC-MS data view

Post by sll022003@gmail.com » May 21st, 2019, 4:49 pm

I am trying to generate a nice image from my offline 2D-LC-MS data. Basically, I fractionated the sample into 50 fractions and analyzed each fraction with LC-MS. In this case, how should I deal with the file input? Some suggestions will be appreciated.

qtao
Posts: 148
Joined: October 7th, 2011, 10:16 am

Re: offline 2D-LC-MS data view

Post by qtao » May 22nd, 2019, 8:49 am

You can use File > Import and Merge with either Column-by-Column or Cut-by-Cut.

The difference between the two modes is that Column-by-Column option assumes continuous scan acquisition (usually in a comprehensive mode). 2D chromatograms imported by Column-by-Column and Cut-by-Cut will look similar, but their RTs are calculated differently.

From what you said, Cut-by-Cut is the one.

sll022003@gmail.com
Posts: 3
Joined: May 21st, 2019, 1:48 pm

Re: offline 2D-LC-MS data view

Post by sll022003@gmail.com » May 22nd, 2019, 11:07 am

Thanks. Since the MS data contain both MS and MS/MS data. After I imported the files, the software used the TIC intensity as the default. Could I change it to use the base peak intensity to show the data in the software?
Plus I also would like to filter the background for the MS data. For example, removing the m/z 371 peaks in the data to highlight the relatively low abundant peaks.

Thanks a lot.

qtao
Posts: 148
Joined: October 7th, 2011, 10:16 am

Re: offline 2D-LC-MS data view

Post by qtao » May 22nd, 2019, 2:21 pm

The Base Peak chromatogram can only be generated during Import by setting Multi-Spectral Filter > Ordinal Limit to 1.

Filtering out a m/z can be done by either of
  • During Import, set Rang Limit to "0-370.5, 371.5-"
  • After Import, View > SIC View to view the SIC, and use File > Save Image As to save the SIC if you prefer.

sll022003@gmail.com
Posts: 3
Joined: May 21st, 2019, 1:48 pm

Re: offline 2D-LC-MS data view

Post by sll022003@gmail.com » May 22nd, 2019, 2:46 pm

Thanks a lot.

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