Mass spec fundamentals - quad parameters

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

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I'm trying to get a better understanding of how quadrupole parameters affect MSD function. Namely, I'm trying to better understand what parameters such as scan speed, frequency, cycle time are and how they are related.

The parameters of a particular method for a GC-MS (Agilent 7890B and 5975) that I use are as follows:

Segment: 2.5
Mass range: 35-260
threshold: 150
scan speed (u/s): 1,562[N=2]
frequency (scans/sec): 6
cycle time (ms): 166.66
step size (m/z): 0.1

Here's what I gather about those parameters, please correct accordingly:

Segment: I think relates to the solvent delay; Time in minutes at which point the filaments turn on and the MS starts collecting data.

Mass Range: m/z range that quad scans over, not too complicated

Threshold: Minimum counts for a peak to be recognized

Scan Speed (u/s): Not sure about this. Software manual describes as "scan speed in u/s" - what is the unit "u"? "N" is the number of "sample points"

Frequency - Number of scans "per cycle" (a cycle is 1 second, I guess?), calculated from cycle time.

Cycle Time (ms): time for one scan to complete

Here's my attempt to tie it all together (this is where I really need help): At the end of the segment, the quad begins changing RF/DC in such a way that each m/z in the range is sequentially allowed to the detector, in intervals corresponding to the step size (so 2250 steps total, for my method). The scan speed is the speed at which the entire range is scanned, so the faster the speed, the higher the frequency and the shorter the cycle time. The cycle time describes the actual time it takes to scan the entire range one time.

The ultimate question I have is, what is the utility of increasing or decreasing scan speed? It seems like there would need to be some compromise between scan speed and how much time is allowed to acquire counts at each mass step. What would be the benefit of increased scan speed? I'm having trouble understanding conceptually how these parameters are related to data parameters like resolution, abundance, etc.

Please confirm or correct my understanding, and please pass along any useful references for this subject.
I think you have a grasp of most of the terms. The reason to increase scan speed or scans/second is to increase the number of scans across a chromatographic peak. Most methods suggest 7-10 scans from the beginning of a peak to the end of a peak. If the scan rate is too slow, then the peak may look like a simple triangle, with a scan near zero abundance, the next at max abundance then another near zero, which does not define the peak well and can lead to erratic integrations. 10-20 scans across a peak will give a smooth Gaussian profile to the peak which will better define the peak and give better integrations.

N=2 means that each mass division will be scanned 4 times and those averaged before it proceeds to the next mass division. Mass division being 1.0 amu or 0.1 amu or 0.01 amu for example, depending on the resolution of the mass filter used. Most are at 0.1 to 0.2 amu resolution, which is plenty for most normal GCMS work, higher resolutions are used mostly in accurate mass studies looking for unknowns more than routine monitoring of a list of analytes. Some software calls the term Averages, I think on Agilent it is 2^n readings that are averaged so N=2 is 4 scans and N=3 would be 8 scans averaged at each point. Higher averages will give more stable results, but then you have fewer scans per peak, so you have to balance the two depending on your peak widths.
The past is there to guide us into the future, not to dwell in.
Thanks for the response James.

So given that I know my instrument can perform 6 scans/sec, how do I know the scans per peak? Aside from judging the peak to have a gaussian shape, do I simply estimate the time over peak elution?

I'm a little confused by the usage of "scan" when you say "each mass division will be scanned 4 times". Is that to say that each step (starting at 25.1, 25.2, 25.3 - for my method) is acquired 4 times? When I think of "scan" I think of the transition of the quadrupole through the whole mass range.

In my instance, the step size is synonymous with the resolution, at 0.1 amu or m/z?
LabRat010101 wrote:
Thanks for the response James.

So given that I know my instrument can perform 6 scans/sec, how do I know the scans per peak? Aside from judging the peak to have a gaussian shape, do I simply estimate the time over peak elution?

I'm a little confused by the usage of "scan" when you say "each mass division will be scanned 4 times". Is that to say that each step (starting at 25.1, 25.2, 25.3 - for my method) is acquired 4 times? When I think of "scan" I think of the transition of the quadrupole through the whole mass range.

In my instance, the step size is synonymous with the resolution, at 0.1 amu or m/z?


You are correct, I should have said each mass division(step) is "read" 4 times instead of scanned. Depending on the mass spec it could be going through the entire scan range 4 times then averaging or reading each step 4 times then advancing to the next.

For the Agilent, if you display the spectra on the chromatogram it should also list in the header the retention them and scan number (8.501 min scan 1275) so if you look at the spectrum at the very beginning of the peak and it is scan 1275 and the spectrum at the very end of the peak is 1285 then you have 10 scans across the peak. When you zoom into the peak you usually see it as a series of straight lines with angled bends across the peak, not a super smooth curve, each of the straight lines is a separate scan. If you look at the spectrum in each scan you will notice the front of the peak will have a bias to lower mass in the spectrum versus the spectrum of scans in the tail of the peak. Agilent scans from high mass to low mass, so as the peak intensity is increasing it scans the low high mass first then the low mass is reading a slightly higher portion of the peak, the reverse is true for the tail of the peak. The best approximation of the true spectrum of the analyte is an average of the center three scans of the peak to average out the bias.
The past is there to guide us into the future, not to dwell in.
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