offline 2D-LC-MS data view

[sll022003@gmail.com]

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]

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]

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]

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]

Thanks a lot.