Dear All,

Is it possible to do MS and MS/MS in a single run in a LC/MS/MS instrument? If it is possible, is it related to any Hardware part or Software part.

Thanks

Yes, and it is related to the software. All the ion traps in our lab can do "data dependent MS/MS" or "auto MS/MS" via the software. The MS does a full scan, then immediately does an MS/MS experiment based on the full scan data and user defined criteria, then this cycle repeats for the entire run. Some software allows "dynamic exclusion", so if one mass has already had "x" number of MS/MS experiments done, it goes on an exclusion list for a user defined amount of time.

Our triple-quads can do auto-MS/MS if you purchase an add-on to the software. Or they can do non-data-dependent MS and MS/MS in a single run without the add-on. If you are thinking of purchasing an MS/MS instrument, you might ask if the software has this capability, or how much extra it costs to include it.

It decided by what kind of experiment you want to do. When we do protein identification by in-gel digestion with the peptide identification by mass spec. We do MS and MS/MS in a single run. Mass spec finds the highest peak first and then switch to MS/MS.

Let me throw a "silly" questions here:

When you do MS/MS, you have collision gas on, what is the timeframe it takes to pump down the collision gas in the MS hardware for you to get a decent molecular ion spectrum, which, probably, prefers a minimum presence of collision gas pressure, thus you have to pump down the collision gas first....

In another word:
MS/MS--> collision gas necessary
MS--> collision gas un-necessary.

thus,
collision gas->MS/MS->pump, pump, pump->MS->collision gas->MS/MS->pump, pump, pump->....

Hope I made myself clear.

I don't think it's a silly question at all. I hadn't ever thought about it, but this would be important on a triple-quad. On the Sciex triple-quads, it appears to take about 5 sec for the collision gas to be pumped out, but that's because the vacuum readout only refreshes about every 5 sec. So it may happen faster than that, I don't know. Maybe someone else can answer it?

On an ion trap (at least the ones in our lab), the helium bath gas is at the same pressure whether you are doing MS or MS/MS, so it's not an issue.

thanks, MG. Sciex people told me you can set CAD (trile Q) at ~8 for IDA experiment (Full scan->ms/ms). I asked them this quesiton, they didn't give me a good answer. I forgot what's Quantum's approach, remembed I asked them that too.

OK, I just thought about it some more with respect to the Sciex triple-quads, and it occurred to me that in Product ion scan mode, even with CAD gas set high, you can lower CE to 5V and get nearly all precursor ion with no fragments, which is what you would want for full scan work. In Q1 scan mode, there is no ability to set CE, but there is the value RO2 that is held at a fixed value for Q1 scans (although an advanced user could change it through the Parameter Settings menu). CE is merely a voltage offset between RO2 and some other voltage in the system, corresponding to collision energy. So if I had to make a guess, I would say that for IDA experiments, RO2 is probably held at some value corresponding to a low CE for the full-scan portion of the experiment, then rapidly switched to a higher CE value for the MS/MS portion. In a plain old Q1 experiment, it is not normally possible to adjust CAD (it is held at some low fixed value like 0 or 1), although I think it is possible to turn it up using the Parameter Settings menu. An interesting experiment would be to turn up the CAD gas to some high value while doing a Q1 experiment, and compare the quality of the spectra to the normal default conditions. I have not done this experiment, but it might help answer your question.

In answer to the original question, it is fairly easy to do MS then MS/MS on the same peak and as stated above it is a software function. We have a Finegan LCQ Deca which is programmable to do this and more (it is too easy to generate enough data to drown in). This is a trap instrument and there is always helium in the trap so there is no need to pump down between detecting the molecular ions and doing the MS/MS experiments. Traps are the perfect solution for these types of experiments, not that there is anything wrong with quads (don't want to start a war here).

Regards,
Mark

xz,

For data dependent acquisitions on the TSQ Quantum (e.g., Full-scan MS > MS/MS), your best results will be when you set the CID gas pressure to less than 1.0 mtorr. A good default that I use is 0.7 mtorr (which also works well for Parent Ion or Neutral Loss scan modes).

Regards,
Kevin

Maybe I'm not understanding the question, but just do your full scan in Q3. You get the advantage of collisional focusing by the CAD gas/collision cell and can leave the gas pressure set at the same value for your MS and MS/MS experiments.