Peak integration issues with masslynx 4.0

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System: Alliance 2795 HPLC coupled to a Waters Quattro ultima running Masslynx 4.0

Aim: I’m trying to obtain a list of absolute peak areas for each of three transitions from data acquired from an MS run

Problem: 1) After processing the samples in Quanlynx I am not able to obtain a summary list of peaks areas for each transition for each sample
2) Only the first transition (number 1 in the compound list of the quanlynx method editor) seems to be integrated for each sample

Detail:
- I identify three transitions for a compound and create an MRM file
- I create a sample list (3 samples) and run the MRM method.
- I obtain chromatograms for each of the three transitions for each sample
- In Quanlynx I create a method in which each transition is entered separately (the compound list has 3 entries). In the ‘General Methods’/’Response’/’Type’ dialogue box I enter ‘External (absolute)’ and click 'area'
- The ‘Smooth’ and ‘Integrate’ parameters I enter as described in the manual with ‘right click/drag’s over the appropriate parts of the chromatogram.
- I then save the method and process the samples ticking only ‘integrate samples’ and entering the method created above
- In the quanlynx browser all I obtain is an integrated peak chromatogram relating only to the first transition (number 1 in the compound list of the quanlynx method editor) for each compound (I can toggle through these chromatograms using the sample toggle button on the tool bar). I created a new method, changing the order the transitions appear in the quanlynx method editor, processed the samples again and, sure enough, the only chromatograms appearing in the results were those pertaining to the first transition in the list
- The peaks have been intergrated but nowhere can I find a summary list. I’ve tried ‘Display/options’ but this only allows the option for list compounds by name or sample #. The ‘Toggle summary’ button in the tool bar has no effect except greying out the ‘show chromatograms’ button
Is there anything that jumps out to anyone as an obvious error or oversight?
And before anyone suggests running standard curves, I’m teaching myself and approaching this one step at a time. At this moment I do not want to complicate matters further and just want to obtain a list of absolute peak areas. At least then I can start some work by using an internal standard and calculate % change from sample to sample which is good enough for basic microsome studies.
Thank you in advance!!
Marcus
I've never worke with QQQ, but have you tried generating a report?
- In Quanlynx I create a method in which each transition is entered separately (the compound list has 3 entries). In the ‘General Methods’/’Response’/’Type’ dialogue box I enter ‘External (absolute)’ and click 'area'


I'm not sure about MassLynx 4.0. In 4.1 more than two transitions from one parent are only possible with TargetLynx. There you can choose Quantification ion and up to five "targets" (equivalent to additional transitions). The compound list needs only one compound using this approach.

However, if you use three compounds as a workaraound, you still can select the peak area to be displayed for each compound, then use "Edit -> copy -> complete summary" to copy all peak areas and additional information you see on the screen, to the clipboard. You will then have three separate tables (one for each coumpound) to work with in excel.

I hope that helps you going further.
Jörg
Thanks for your suggestions chaps but I did actually manage to find a solution and this should help anyone else who may have similar problems with Masslynx 4.0 (If anyone still uses it.....i didn't realise how old this software is and that no one seems to be using it anymore!).

There's a bug in the program which means the peak area summary table can sometimes become un-pinned or floating within the quanlynx frame and can actually become lost such that even using the summary toggle button will not retrieve the table.

In such a case shut down Quanlynx, find the file 'quanlynx.~ql' in C:/MassLynx and delete it. Re-process your samples and the table should appear
I need help. am running a ZQ mass spectrometer using masslynx 4.o. My problem is that mass spec does not acquire when i run the method from sample list. I have checked for possible hardware malfunction but i don't have any. contact closure board is fine, hplc is communicating well and i have control. masslynx main page keeps indicating 'waiting for inlet' and also 'MS tune page'.
Has anyone experience this?. help. Am using agilent 1100 hplc.
Try to kill the "Inlet kernel" and "Inlet editor" processes using the windows task manager. Then start the inlet editor from masslynx main page. This helps in most of the cases for Agilent 1100 and MassLynx 4.1.

Good luck
Jörg
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