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Topic: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!) (Read 788 times) previous topic - next topic

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

Reply #15
Thanks, Romanas!  And so you recommend for us to use proteowizard to convert our files and not use ABF converter?

Also, we usually do not acquire anything from 0-0.2.  It just goes to waste.  And so, just to be clear, currently, there is no remedy yet for this.  I am glad we found the culprit but too bad there is no remedy yet.  What is the process for requesting this for MSDial?  Thanks and keep safe.

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

Reply #16
HI Romanas,
  I tried using proteowizard and just only focusing on data from 50-500 seconds.  But unfortunately, I am still seeing the high %CV's. This is a bummer.  I have included the picture of the proteowizard parameters and also some of the amino acids that normally had low %CV's (phenylalanine and glutamic acid) using Masshunter but I am still seeing high variation in MSDial.  But when I did just regular MS1 without any deconvolution, I am getting really good %CV's. 

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

Reply #17
Hi Marites, instead filtering by seconds in ProteoWizard, filter by scans. The key point is to set the beginning of the filtering range so that output file matches the MS-DIAL settings.

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

Reply #18
Thanks, Romanas!  Can you please guide me as to how to filter by scans instead of by seconds?  I have not done this before.  How would I get the # of scans at 0.25 minutes?  I have the acquisition rate which is 4 spectra/seconds, which means there are 60 spectra at 0.25 minutes.  Should I then filter from 80 scans - 2000 scans?  I chose 80 just to make sure I am out of the inconsistent range.  Thanks!