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Definitely there is an effect. Both for LC and for mass spec. You may find differences in retention, including changing the elution order of certain compounds. The biggest change usually relates to the addition of pH modifiers, and ion pairing agents. Trifluoroacetic acid is great for LC, but causes severe suppression in MS. Switch to acetic or formic acid instead. Non volatile buffers (and even volatile buffers such as ammonium acetate) can also reduce signals. EsI is aided by volatile solvents, so be sure when switching from methanol to acetonitrile that you still have an appreciable amount of organic (20% or more) to maximize signals.

Thanks for your question. Historically, tandem ms was built on triple quads. And it also serves as a good starting point to teach the concepts. But newer MS platforms seem to be taking over. A good example is a QqTOF, which simply swaps the last quad for a Time of flight. This machine can do anything a triple quad can do, and more (specifically, high res MS, and faster scanning). Orbitraps are also taking over the industry, and also can do the same job as triple quads and then some. Keep in mind that Orbitraps also involve other components that roughly mimic a triple quad (I over simplified the full platform). So, to sum, yes, many other instruments can perform the types of scans available to triple quads. Including the orbitrap.

Wow, great question! Technically, the ion being fragmented in a triple quad is different that in a gc/ms experiment. That's because ESI usually protonates our molecule while EI deals with a radical ion, missing one electron. It may seem like a subtle difference, but the way radicals behave will be different. You tend to see similarities in these spectra, although with ESI the fragments are also shifted up by 1 u.

@@shortchemistry7927 Thank you for the answer! So would a tripple quad give enough fragmentation do be able to do structure elucidation (at least of small molecules)?

@@Ambient_Scenes Most definitely. Any system capable of tandem MS could be used. Or a system that creates fragments through ionization (EI)

@@shortchemistry7927 Thank you for the answers!

I would say that really depends on the specific goals of the analysis. Are you looking for purity? Stability? Sensitivity? Throughput? Personally, I am excited by what top down proteomics can offer, which implies instruments with high resolution and alternative fragmentation beyond CID. So for that, you're looking at Orbitrap or FTICR (possibly QqTOF). But a conventional QQQ will be great for MRM assays. In terms of vendors, everyone has their favorites. And certainly, each has their advantages. I think establishing a relationship with the vendors, to see how they can assist in terms of training, technical support, upgrades, and ancillary equipment etc... should all factor into a buying decision.

Good question... because normally we think ICP breaks everything up into single atoms. So what is left to fragment? Well actually, ICP doesnt always break up everything so you can still be left with a few specific molecules (ie polyatomics), with a mass that coincidentally is the same as your analyse. These interferences are a big problem and need to be eliminated. Enter MS/MS, which allows you to break up the polyatomic compounds and basically allows you to separe the signals of the good stuff vs the junk in the background

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