https://www.openchrom.net/

http://www.mmass.org/

AMDIS

Hi Markus Christ, thanks for your suggestions. I have tried openchrom previously and find that it isn't appropriate for my needs as it lacks deconvolution functions.

Hi Grzegorz Boczkaj, thanks for your suggestion also. AMDIS throws out too many false positives for it be any use I find.

Also, I'm not adverse to using R for analyses if there are any suitable packages available.

Chemstation? But it's not free.

what kind of difficulties you face while using MassHunter ? is there any? let us discuss, me too using MassHunter

Hi Ritesh,

Thanks for your response. I’m having issues with peak integration and baseline removal.

Thanks,

Joe

Hi Joe, please be specific when asking for suggestions. What are you trying to do and what difficulties did you face? Are you using the default parameters or are you still having troubles after tweaking the parameters and protocols?

Hi Gang Chen,

Thanks for your interest in my question. With regards to the difficulties I am facing, they predominantly lie in baseline subtraction, peak integration, and mass spectrum deconvolution. I have tried using the deafult parameters, but am unsure as to where to begin with tweating parameters and protocols in MassHunter B8.0.0.

Best wishes,

Joe

I am not familiar with version B8.0.0; but from my experience with B2.0.0 and ChemStation, the default parameters are overly sensitive and you get a lot of "grass" on the baseline. Try bigger numbers on slope (default 1, change to 100), minimal peak height (default 1.7, change to the half-height of your smallest real peak), and peak area (default 1, change to 10); then smaller peak width (change to 0.05-0.1). There are also multiple selections on the baseline detection, just play around and see if one of them produces better results. You can always call their technical support line and they are really good at walking you through the optimization processes.

Hi @Gang Chen,

Thanks again for your informative reply - I will have a look at altering some of these settings. What I am finding is that there is little explanation of what they actually correspond to or explanation of baseline detection. Having spoken to Agilent UK I have found them to be quite unhelpful with regards to offering advice on this matter.

Thanks,

Joe

In QQQ Quantitative, Use UNIVERSAL integrator and change parameter threshold and peak width.. if u want do that a certain peak,then use timed events table and add RT and give particular event..regarding blank subtraction it can be done in Qualitative navigator..

Hi Joe,

running "ClearView" from Markes before using the MSDchem or Amid will greatly improbe itegration due to a properly corrected baseline for integration by the MSDchem software as well as identification by Amdis 32/NIST-14 or NIST 17.

From my earlier tests with "OpenChrome" I also fond this software to be not very useful and a suitable replacement for Agilents "MSDchem G1701 FA".

Best regards, Peter

Hi Peter Behrend,

Thanks for your reply. I had a look on the Markes website and cannot seem to find the piece of software you recommend?

Best wishes,

Joe

Hi Joe,

this is the Help picture I obtain from my own program copy from 2009.

Originally, it's an ALMSCO software, which I bought from a German representative early 2009.

Hi Joe,

please have a look at "ALMSCO Software products" ...

Actually, Market sells a combined software pac "TARGET VIEW".

This pac consists of "Clear View" plus a MS-Target application.

At least from my point of view "TargetView" as a complete Pac ist only meaningful for GC/MS beginners, not aware of all the extra functions of 'AMDIS'.

While a 3 machine license of 'ClearView' ist still (after 10 years usage a valuable help in daily work, I returned the Test Copy die to insufficiant value for the experienced user afer a 30 day trial period.

However, this estimation from me ist of course dependent, what you expect from the software !!

Best success and greetings,

Peter Behrend

I missed the information about AMDIS, which is a freely available and sophisticated  software for GC-MS data interpretation from NIST. AMDIS does a complete analysis of noise and performs also a correction for baseline drift

In my eyes it performs an acceptable mass spectrum deconvolution even for complex mixtures and is able for extraction of closely coeluting peaks. It is therefore a good approach for target and non-target analysis.

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