Setting Up Parameters in Quant Methods -- MassHunter Quant 12.0

Hello everyone,

It is my first time using MassHunter Quant (version 12.0), and I have some questions regarding setting up parameters in quant methods. These questions might be very basic. Thank you in advance for the help.


Question 1:

Is there a way to integrate all peaks within one acquisition window, and calculate the concentration of each peak without having to define each individual compound please?

In the attached screenshot, there are over ten target peaks in one window. The predominant peak in green is a toxic compound, included in the calibration curve using the average RF method. The other peaks, non-toxic compounds, do not require individual naming, but their concentrations are calculated using the RF of the toxic compound in the same homologue group. Rather than setting up over 10 single compounds individually, assigning them with the same compound group and adding them into a total compound, is there a way to establish a total compound only and have the software integrate all peaks within a specified RT range?


Question 2:

How can integration parameters be configured to include multiple coeluting peaks as one peak?

Some analytes are coelutions, so we need to include multiple peaks as one peak as shown below. Is there a way to set up integration parameters to achieve this and save time on manual integration please?


Question 3:

Is it mandatory for a Qualifier to exist in the method?

We have some targets that are known with very low responses for the confirmation ion, and therefore, we ignored them in our SOP. Is there a way to delete the Qualifier row in the quant method?

Question 4:

How does the software calculate noise if “Noise Regions” column is left blank? Will the software automatically identify a representative piece of noise within the acquisition window?


Question 5:

How to calculate sample-specific detection limit (SDL) for each analyte please?

Our SDL formula is SDL = a factor (2.5 or 3) * Noise * average RF of that compound from the Calibration Curve.

Which column should be used for this calculation?

Any help would be much appreciated!

  • Question 1:

    There isn't a way to integrate all of the peaks within a window and then calculate the concentration based on the RF of one of the included peaks. You will have to set up those compounds individually and then use compound groups/math.

    It would be possible to set up the scenario you describe with the Spectrum Summation integrator (more below) if there wasn't an overlap in retention times, like I see in your example.

    Question 2:

    If you go into the Method Editor -> Advanced Tasks -> Integration Parameters Setup, click on the right-side of the Int. Parms. to bring up the integration parameters and choose the Spectrum Summation. The next step is to specify the Spectrum Summation parameters that you want to use to create the peak. Spectrum Summation allows you to specify a baseline, a retention time (RT) or a delta RT, and specify how you want the retention time reported.  

    Question 3:

    Yes, you can delete a qualifier row if you want. Highlight the row and right-click to get a menu that has a Delete option.

    Question 4:

    The noise regions are determined by the chosen integrator. The Quant Help explains that the noise region is calculated by a statistical algorithm and can be displayed in the extracted chromatogram when a parameterless integrators, like Agile and Agile2, is used.  If either of the parameter-based integrators, General or Universal, are used the noise regions will be between the peaks and are not displayed.

    Here’s an additional post that has some more information on the noise calculations:

     Question 5:

    This would be a custom calculation that would require extensive programming. If you’re interested in more information, the answer here may be helpful

  • Wow! Thank you so much for your help!

    Can I please ask one more question here?

    Where shall I input the text of the units for Final Concentration please? For example, in my method, the unit is defined as "ng/mL"; however, the units for samples are in "ng/L" or "ng/g". Which column would you suggest being filled with this info (the text of units) in the batch table, so the units for samples can be finally parsed into LIMS please?

  • Hi  

    Units are set in the concentration setup in the method. You can specify the units by typing in the units field as your units aren't already listed.

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