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MSSTRING() and decimals

Posted: September 9th, 2019, 2:51 am
by sundberg
I'm trying to export a blob table which includes the mass spectra in text format using MSSTRING() with a CLIC-expression. It works, however it only exports the mz values with 1 decimal. I'm using the mzDecimal option, i.e. full command is MSSTRING("mzDecimal=4") as described in the manual. We're using GC Image 2.8, HRMS-edition. Mass spectra of pixels/blobs etc all show the correct mz values, data is collected on an Agilent 7200B QTOF. Any ideas?


Re: MSSTRING() and decimals

Posted: September 9th, 2019, 9:14 am
by qtao
Try the following expression

Code: Select all

If m/z values have the correct decimal places, check if Configure > Settings > Multi-Channel > MS Data Binning settings are set to By Integer Intervals.

If m/z values still only have one decimal ".0", it is probably because there is no centroid data. You can double check the Point spectrum shown alongside Profile. There is no existing CLIC function that can be used to retrieve profile spectra. But, a script written in a CLIC plugin could get this done.

Re: MSSTRING() and decimals

Posted: September 12th, 2019, 1:40 am
by sundberg
The m/z values show .0 as decimal, with MS Data Binning is set to Integer intervals. The data have been collected with in both profile and centroid mode, and we can see both when looking at blobs/pixels... Is there someway you can force import to only include the centroid spectra? I have attached screenshots of how it looks.

Re: MSSTRING() and decimals

Posted: September 12th, 2019, 8:54 am
by qtao
The software always imports centroid data if it is available. If centroid data is not available, the software will import nominal spectra of profile data. From the screenshots, there are centroid spectra. So, the only problem is MS Data Binning setting.

By default, MSString() uses the Blob spectrum. Blob spectrum is the sum of all spectra of a blob. During summation, average m/z values are calculated based on the binning settings. Choosing a non-Integer option should resolve the problem. If you are not sure which option, choose Adaptive Bin with 0.5mu tolerance. You can find more details here.

Alternatively, you can use MSSTRING@peak("mzDecimal=4", "intensityDecimal=0") to get the peak spectrum. It will return the centroid spectrum at the apex of a blob. Since it is just a single spectrum, no binning is required.