Peak Integration Algorithms… Hmmmm Which one to use?

This is a question that comes up almost daily. So from the perspective of someone who has been using many flavors of mass spec software, none of the choices of any vendor is exactly ideal.

Here in Thermo our two most commonly used detection models are Genesis and ISIS.

Now somewhere in time, the naming convention got lost and it’s hard to know which one to use in the right situation.

So here’s 10 years of experience in using these, in many forms of data.

Genesis is good for detection of peaks in a noisy baseline. Typically in full scan types of data collection. So Single Quads, Ion Traps, FID and PDA data sets.

I use these points typically as a good set of default values: Nearest RT, Smoothing of 3,  and signal to noise threshold of 5.  The rest of the values can be used for fine tuning but these are my basic starting points.

ISIS is good for more abstracted data with cleaner baselines. Typically SRM, SIM and CRM scan types of data collection. So Triples Quads, MS3 systems, and Exactive instruments.

Here I typically use a set of values of Smoothing 3, Area Noise factor 5 Peak noise 10 Baseline window 40-80(just depends on how noisy it is)


MINIMUM PEAK WIDTH – This really comes into play when dealing with different types of chromatography. Narrow peaks I use 3-5 (scans) as my minimum. So GC and UHPLC types of data. For LC/LCMS I use typically 20( scans), because these chromatographic peaks are wider and usually noise peaks are much narrower.

Again this is a rule of thumb and a starting point.


Happy Quan.

About humphrjk

Product Manager for Analytical Software for Chemist. Analytical Chemist, Mass Spectrometry Scoutmaster Troop 4277 Skipper Ship 4277 Vice Commodore Texas Sea Scouts

Posted on April 25, 2012, in General Use, Method Development. Bookmark the permalink. Leave a comment.

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