Low Sensitivity within MassHunter

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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I am having an issue within our new MassHunter system, and am showing very low sensitivity with my lowest standards in my curve. My upper level peaks look great (highest level is 5000ng/mL, lowest is 10ng/mL), but my lowest peaks are hard to integrate as they are flat and have extremely low area responses. I am running PAHs, and here are some of my parameters:

Pulsed Splitless
Temp - 300C
Liner - Low Pressure Drop Liner with Glass Wool
EPP Ref Temp - 80C
EPP Initial Pressure - 11.5 psi
EPP Initial Hold - 0 min
EPP Ramp 1 - 98 psi/min
EPP Final Pressure 1 - 80 psi (constant flow mode)
EPP Pressure 1 Hold - 0.3 min
EPP Ramp 2 - -98 psi/min
EPP Final Pressure 2 - 11.5 psi
Carrier (Helium) - 40cm/sec
Carrier Flow - 1.2 mL/min
Time ON - 1.8 min
Split Flow - 40 mL/min

Oven Temp:
Initial Temp - 80C
Initial Time - 1.0 min
Ramp - 12C/min
Final Temp - 350
Hold Time - 3 min

Interface Temp - 300C
Source Temp - 250C
Quad Temp - 150
SIM mode
Relative EMV Voltage
4 min Solvent Delay
Column: DB-5MS 0.25mm x 30 meters x 0.25um

I was going to upload some pictures of the peaks, and maybe can if need be. Basically though, I am getting flat pancake peaks for my lower levels, but nice sharp peaks for my upper levels, and my responses for some of my compounds are tiny (example: area response = 29). Anyone know if there is a setting that is different between MassHunter and ChemStation that I am forgetting or missing possibly? MH is a new system for us, and am still trying to figure it all out. I have checked the connections between MS and injection port, and all look okay, plus ATune looked fine as well with everything passing and looking similar to tunes I had ran before we switched over to MH. I have ran MH with no problems for a few other methods I run (on different instruments though), but for my PAHs they just aren't quite working the same. We did just have the HED power supply replaced as well, and source was cleaned less than 6 months ago, and has not been ran on much since the MH install. Any help or ideas greatly appreciated! Thanks!
Unless i'm missing something, Masshunter is a software package to process Agilent LC/GC-MS/(MS) data. Using this versus another software package (chemstation) shouldn't make a difference in peak shape/height. Unless you're overly processing data (such as smoothing)..

Can you start with telling us the system that you use?

With the information that you gave, I suspect this is a tailing problem due to active sites somewhere between your inlet and MS. Higher concentrations always look sharper if you have a tailing problem. PAHs are very susceptible to this. You need to make sure you have a clean, leak-free, system from injection port to MS, and clean cuts for all column connections.

Posting a chromatogram always helps!
1.8 minutes splitless is a little long for 300C injection port temp. That can lead to more tailing, though it does increase the amount on column of the highest boiling PAHs. Try with 1.0 min splitless time and see if that helps the peak shapes.

It usually is something causing some tailing which distorts the lowest concentration peaks the most, once you get above the tail the peaks look sharp. I would also not use the low pressure drop liner when doing splitless injection, that just gives a little dead space at the bottom of the inlet for more tailing to occur. A good single taper liner with glass wool at the bottom works best for PAHs. And make sure the column is only about 1mm above the gold seal. You can do this by taking a gold seal and sitting it on the column/nut/ferrule combination and checking the height before you install it into the inlet. I keep an old seal handy just for this, check and mark the column then set the seal aside and install the column in the inlet. Works great to double check the column depth.
The past is there to guide us into the future, not to dwell in.
Two ideas for you here.. make sure to read down to the bottom, as I think the second point will have a bigger impact on solving the problem.

Peak areas are smaller in MH Qual data analysis than in G1701 MSD Chemstation DA. The drop is proportional, but if you integrate a data file in MSD Chem DA using the chemstation integrator and then reintegrate the same data file in Qual using the universal integrator you'll see that the calculated area is smaller by a factor of 10.


MSD Chemstation DA F.01.03
File: evaldemo2.d
Integrator: Chemstation

Peak 1: RT 5.254, Area 36,233,062
Peak 2: RT 6.671, Area 51,138,541
Peak 3: RT 7.965, Area 44,436,966
Peak 4: RT 9.794, Area 24,853,244

Qualitative Analysis B.07.00 SP2
File: evaldemo2.d
Integrator: Universal

Peak 1: RT 5.254, Area 3,640,717.8
Peak 2: RT 6.671, Area 5,127,358.7
Peak 3: RT 7.965, Area 4,457,331.86
Peak 4: RT 9.794, Area 2,530,384.17

MSD Chem DA has two integrators: RTE and Chemstation. Chemstaton is intended for higher frequency data (ie, GC detectors that operate at 20 hz). The RTE integrator (which gives basically the same numbers as the example above) is intended for lower frequency MS data (2-5 Hz.)

MassHunter DA (Qual and Quant) have several integrators: Chemstation, General, Universal, MS/MS, Agile, and Agile 2.

The equivalent of the msd chem integrators in qual/quant is Universal. And it was scaled to give an equivalent magnitude as the other integrators, which is the reason for the 10x scaling factor.

This may explain that a peak that usually gave you an area of 390 is now showing up as 39. You can view your SQ data generated on this instrument in the old software and do some comparisons to make sure. It is possible to use the data translator to translate data acquired with old software to be viewed in Qual/Quant. If you take data generated in masshunter data acquisition you can load it in msd chem DA without a translator.. so either get one of your old data files and translate it, open in qual OR take a new data file back to your old data system (if you've still got it) and integrate it in msd chem da.

The data translator is installed from the gcms supplemental disk that came with the software, it may already be installed on the PC and be available in the start menu.

Just a note about the translator: inside your data file you will have an ms signal stored as data.ms. There will also be an AcqData containing mspeak.bin and msscan.bin msscan.xsd and some other files. MSD Chem DA reads the data.ms, Qual/Quant read the contents of the AcqData folder. Its the same spectral data recorded in two formats. The data translator will read the data.ms and convert it into the MassHunter AcqData format.. that is why you would have to translate old data for it to be usable in qual/quant.


If your problem is literally reduced response and not just that the area counts appear low in the software I think I've got a couple recommendations that can help.

You're running PAHs, which are sticky. Increase your source temperature to 300 C and get a 6 or 9 mm draw out lens (if this is an inert source, if it is an extractor source the equivalent lens you would need is called the extractor lens.) The wider diameter lens will prevent analytes from adhering to the surface of the source. You may observe lower abundance of your less sensitive analytes, but more thermally sensitive/inertness sensitive compounds such as perylene and chrysene will be much higher abundance and more linear across your entire range. Low end calibration non-linearity is a common problem in PAH analysis.

Changing the lens is cheap, and the majority of your compounds will respond better. Any drop off in some of the good actors is no big deal.. you'll still have plenty of response. Restek has some good pictures showing the benefit: https://blog.restek.com/?p=13930
Thank you all! Sorry for late response, but I will try a few of those ideas out! I am using a 6890N GC and 5973N MSD, but I cannot change any other method parameters that I listed due to it being a validated method and I cannot deviate from that unfortunately for my samples. I ended up moving to a different instrument for the time being (with a 7890 GC), where my sensitivity and peak shapes have greatly improved, but am having issues getting my standard curve to pass now (separate issue).

I am planning on discussing with my supervisor to at least get either a 6mm or 9mm draw out lens and trying that on that instrument, which may help. I have been using the Agile2 integrator within MassHunter, and switching to Universal hasn't changed my values at all, but we are using MHQuant, not MHQual too. Thanks again everyone! If you have any other ideas, let me know, otherwise I will keep trying different things to see if it may help.
Try using the General integrator, I believe the values it returns are more like those of the older MSDChemstation.
The past is there to guide us into the future, not to dwell in.
Agile2 is also fine, as long as your chromatography is good the algorithm should find the peaks. I assume you're working in quant?

Low sensitivity could be a number of things from sample prep to instrument maintenance. You should post some data files (zip them up and upload them somewhere) or screenshots.
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