“I have not failed. I have just found 10,000 ways that don’t work.” – Albert Einstein

Many people compare chemistry to cooking.  If you follow the directions, you’ll end up making a tasty cake.  In some aspects of my project, this is accurate.  However, the extended kinetic method has so many more nuances than a simple recipe.  Regarding the experimental part of my project, there are two sections: solution-making and data acquisition.

The instrument that I use, a triple quadrupole mass spectrometer, can collect data for a solution in mere minutes.  This part of the procedure is incredibly straightforward.  The challenge of the kinetic method lies in the solutions.  This requires making and diluting solutions for analytes, references, and heterodimer solutions.

Typically, when I begin experimentation on an analyte, A, I make 1E-2 M and 5E-5 M solutions from stock solutions.  In addition, I make similar solutions for each reference (B, C, D, etc.).  To create the heterodimer solution, I make a 1:1 solution of the analyte and reference, with 1% formic acid (usually, 1 mL of analyte and reference and 20 uL formic acid).  That last solution is then injected into the triple quad and the spectra is observed in Q1 mode.  The goal in this mode is to see a substantial heterodimer peak.  The molecular weight of the heterodimer is determined by adding the molecular weights of the analyte and particular reference, plus a hydrogen atom, A-H-B.

Once the heterodimer peak is isolated in Q3 mode, varying collision energies are used to collide the dimer into fragments.  The fragments I’m specifically looking for in this mode are the protonated analyte peak and the protonated reference peak.

Several problems can, and often do, arise in the data acquisition process.

1.)  There is no substantial heterodimer peak visible in Q1 mode.  This often occurs when there has not been a significant production of the heterodimer.  At this point, higher concentrations of both reference and analyte are often needed with which to create new dimer solutions.  Too concentrated solutions must be avoided, as this can cause the triple quad capillary to become clogged.

2.)  There is an incredibly large analyte or reference peak in Q1 mode.  This can sometimes occur in conjunction with the first problem; there is a large excess of a reactant when producing the dimer.  A solution to this problem includes varying the concentration in the 1:1 dimer solution.  It may be necessary to decrease the concentration of one reactant in order to again avoid clogging the instrument and to get comparable analyte and reference peaks.

3.)  There are numerous additional peaks in Q1 or Q3 mode.  In Q1 mode, a large amount of background noise can be attributed to impurities in your solution or residual ions from previous runs.  Additional flushing/unclogging of the instrument or making a new dimer solution is sometimes required.  In Q3 mode, additional peaks may be a result of secondary fragmentation of the dimer.  While this is not a procedural error, these additional peaks need to be taken into account when working up the data.

A big part of the learning process comes from mistakes and problems.  As I become more familiar with the kinetic method and the triple quad, assessing and fixing these problems will become easier.

– Kathy


  1. nvhudsmith says:

    I hear you on the pain of making solutions — I rarely make such dilute solutions, but when it comes up it is often frustrating. But I agree that is probably one of those things that comes with practice and experience in lab. Sort of like having a “feel” for something, and of course, you have to have a “feel” for some more complicated fancy-pants souffle recipes, and such. 🙂