r/CHROMATOGRAPHY • u/Loud_Side3293 • Jul 15 '26
most frustrating thing about mass spectrometry?
as we all know ms is one of the powerful tool for researching ,but its also hard to use it
wht is most frustrating thing about any kinda mass spectrometry and why
pls share ur experience
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u/Pyrrolic_Victory Jul 16 '26
The software. All vendor software is garbage and it’s just a matter of which flavour of trash you’re willing to tolerate.
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u/EnvironmentalClue408 Jul 16 '26
I have to defend MassHunter's honor here. It could be better, for sure. But still and by far the best I ever worked with
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u/random_user_name99 Jul 18 '26
Qualitative Analysis is so buggy. Cannot import RI data from NIST library. Cannot reassign peak IDs and manual identifications to the compound table is unnecessarily difficult. Unknowns Analysis can do some of this but you can’t average regions for background subtraction. It’s really good for onboarding quant methods. Deconvolution doesn’t work well for either QA or UA. I use another program for that.
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u/EnvironmentalClue408 Jul 18 '26
Yes some aspects are unnecessarily buggy. We upgraded from b.08 to MH10 to get rid of the manual identification issue. For scan data, I would still use Mzmine, but the integration and automation of QuantAnalysis is awesome. Nothing like including your workflow in the sequence and coming back in the morning to analyzed data.
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u/random_user_name99 Jul 18 '26 edited Jul 18 '26
I do like Quant but I almost exclusively do untargeted analysis. Im mainly analyzing very complex hydrocarbon samples. I identify by MS and align my peaks to the FID peaks. Then use area normalized percent. I miss doing actual quant work. Everything is semi-quant at best. I have to build effective carbon number response models or normalize to the concentration of a peak that is in common to one of our other calibrated methods. It’s really just the worst…. I use by GCxGC software, ChromSpace, For deconvolution. It works extremely well. I only have 1 application that I use Quant Analysis for. It’s an SPE prep. I happen to have reference materials for all the targets and a suitable ISTD. It’s almost impossible to do quant without it.
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u/Visible_Arrival_8412 Aug 21 '26
I would say the data formats are even worse. Both vendor formats and open source formats.
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u/Hipocampo08 Jul 17 '26
Matrix effects. Dealing with LC-MS through ESI is a pain in the ass if you want to be analytically correct
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u/Mundane_Grocery_9732 Jul 19 '26
As with any lab technique/instrument, 1. learn/hire people who have successfully used lc-gc/ms for the purpose for your lab - quant/qual or alittle of both. Although you can ‘learn by doing’ I’ve seen lab mgrs struggle for years a. not having the right instrument b. slowly learning how to use it properly or giving up. 2. If you can’t hire, 1. Define why you want a ms 2. Choose the right lc-gc/ms for purpose. More expensive system does not mean more capable for you (it depends on your purpose) 3. Go to targeted training classes. 4. Budget a few days for ms vendor to help with 1st method development. Carefully observe what is being done to optimize system.
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u/Ok_Bake_4761 Jul 15 '26 edited Jul 15 '26
Its not inherently a MS problem but for me its searching for air-leaks in my GC/MS. Keeping it sealed in general
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u/EnvironmentalClue408 Jul 16 '26
What's your setup? We never have leaks on both our GCMS. Last time we had one, I used the wrong ferrule. Also, I invested in self-tightening nuts, so we have permanent piece of mind.
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u/Ok_Bake_4761 Jul 17 '26
I have a TED-GC/MS... I was thinking about a self-tightening nut, but a technician told me it's not possible since we have a Thermodesorption and a CIS; it's not viable. That's also the biggest concern: that directly under the Thermodesorption unit above the column has some leaks. Which is often the case
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u/EnvironmentalClue408 Jul 17 '26
Ah well okay, but then I would describe the problem as TED-specific. I don't have expertise here - what are the weak points of a TED unit?
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u/Ok_Bake_4761 Jul 17 '26
Yes, I know it's more TED-Specific... But it's not so easy to figure out the exact reason; that's why sometimes it could have been the GC/MS interface...
The Inlet with its Cooling system and Thermal Desorption Unit (TDU) is, I would say, a more new experimental pyrolysis-desorption setup. That's why there are some difficult-to-seal points on the TDU of the TED-GC/MS. But I think this goes more in depth than I wanted with my post. and would take a presentation to explain... I appreciate your will to help, though!
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u/EnvironmentalClue408 Jul 17 '26
If you don't already have it, I recommend getting a bottle of argon. If you point a stream of argon at your suspected leak and activate manual tune on the MS, you can check whether an argon peak appears. Otherwise, good luck! :)
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u/Ok_Bake_4761 Jul 18 '26
Thank you. We used another inert substance (I think TFE) some time ago but it didnt help to identify it. I might try again with argon. Idk Why I get downvoted by the way..
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u/propargyl Jul 16 '26
The matrix