Why the MS data? An analogy

Here's an analogy, it may not be great, but it's what I've got.

You have some buckets of balls ("molecules"). There are ping-pong balls, whiffle balls, swedish meatballs, baseballs, Momma's big meatballs with ground beef, Momma's meatballs with beef and breadcrumbs and basketballs.

You are trying to determine the whether the batch of Momma's meatballs has more with breadcrumbs, or more without (the carbon isotope ratio).

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You are standing on a very high tower, and dropping the balls all at once onto a conveyor belt. The balls that land first are near the beginning of the belt, and the ones that land later are further along the belt.

From experience, you know how long it takes Momma's meatballs (the 5aA molecules) to land from the start of the belt, and how long it takes swedish meatballs -- they are quicker. The belt is moving fast enough that Momma's meatballs with crumbs are a little slower than the ones with all meat.

You drop the balls, and then you count the number of impacts around a spot on the belt corresponding to the time you expect. These counts are your "peaks".

With well separated peaks, the splats of the breadcrumb meatballs don't overlap the ones with meat.

So you count the number of splats around your peaks to decide what the ratio of meat to crumby meatballs is.

If there are no other balls in your bucket, this can work well enough. But if you've got baseballs and golf balls, and other odd molecules, you may find some of them landing around the same places as the meatballs.

If you don't recognize this, you may count baseball impacts as beefy-meatballs, and mess up your ratio result.

In Gas Chromotography, the impact time is called "elution" time, and when two different molecules impact at the same time, you have "co-elution".

The way you tell if you have co-elution is to collect the weights of the fragments that come off the conveyor.
The meatballs splat in a predicatable way that is very different than baseballs. If the mass of fragments (ions) looks like there are a lot of baseballs, then you have "matrix interference", and you know you can't rely in the impact counts.

When looking at a complex urine sample, you need to be very sure you don't have co-elution by checking the mass-spectra at the same time.

Getting that MS data is what this argument is about.

Look for the comments to this post, where all the pedantic corrections will be. It's an analogy folks!