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Topic: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!) (Read 424 times) previous topic - next topic

MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Good afternoon!  I have run a calibration curve and each levels were injected 12x for replication in Agilent 6545 QTOF All ions mode.  I used Masshunter Qual to identify some molecules from our standard mix  and then compared this to MS-Dial. We were hoping to use MS-Dial with our future untargeted data analysis but this is just proof of concept on checking data quality between MS-Dial and Masshunter Qual/Quant from Agilent.


Sample info:

Calibration curve in methanol: 0, 0.05, 0.1, 0.5, 1, and 2 ppm with 12 injections each levels and ran this in All ions pos and neg in Agilent 6545 HILIC chromatography.

Problem:   I am seeing high %CV's from MS-Dial analyzed data than in Masshunter Qual.  I was hoping MS-Dial would give the same if not better quality than Masshunter Qual.  Can some one please check my parameters?

For example, at 2 ppm for Arginine neg mode, we are seeing 8.4% CV while in MS-Dial we were seeing 90% CV!!! The retention times were comparable between the two data analysis tools.  What is causing MS-Dial to have such high %CV?  Your help would very helpful.  Arginine and Methionine calibration curves are shown in the attached files.  Thank you and looking forward to your response.   Keep safe!


Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #1
how do your extracted ion chromatograms look for your compounds of interest in MS-DIAL? maybe you need some smoothing? are you picking up correct feature for your calibration curves?

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #2
Hello!  Thank you for the reply.  I ran my samples in Agilent 6545 and so I used their tool to extract the ion chromatograms.  And so I know that the peaks are there consistently but MS-Dial is not picking them up consistently.   Hence, I am getting noisy data.  I have sent my MS-Dial parameters in the attachment.  Can someone please check them?  Thanks! 

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #3
can you share a raw data file (google drive, dropbox etc.) to reproduce the problem with your MS-DIAL parameters?

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #4
Hello!  Ok.  CAn you please send me your email address so I can put in the dropbox and send it to you?  Thank you!

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #5
HI Romanas!  Good morning.  =)   I just sent you 6 files of negative mode all ions data.  These are separate injections of 2 mg/L standard concentration from different vials.  Please keep me posted.  Thank you and keep safe.

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #6
I think the problem is the SCAN order (e.g. use mzML to check in SeeMS from ProteoWizard or MZmine). We are also using Agilent QTOF - the MS files start with AIF scans. Try the experiment settings as in attached screenshot.

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #7
Good morning, Romanas!  Thank you.  I will try that.  But I am seeing that you are not getting reproducible EIC for phenylalanine either using MS-Dial even with the new experiment setting.  Can you please verify?  Should I send a non-converted files?  I appreciate your help with this.  Thank you, Romanas!

Please see attached picture of the EIC of phenylalanine from masshunter.





Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #8
Hi Romanas,
  I did what you have asked me and I am seeing the same irreproducibility.  Please check my attachment.  Maybe I should check the converter.  Thanks!

Marites

Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)

Reply #9
Hi Marites, can you please send the original .d files? The height/area might be slightly different due to smoothing parameters/integration in different softwares. What do you exactly mean by "irreproducibility"?