precursor and fragment relationship in .mzml file

Hello jamie.dixon ,

Precursors ions typically have multiple fragmentation pathways. The resulting MS/MS product ion spectrum contains all possible fragments for a given set of conditions, so you cannot verify the mass of the precursor by summing the mass of all the product ions. In many cases you will not be able to find the corresponding complimentary piece for a given fragment, as the resulting ion may not be stable.

One tool you may want to consider trying is the MassHunter Molecular Structure Correlator (MSC) Software. This is available on the supplemental software disk that shipped with your QTOF. The guide is available online at the following link and explains some of the basic concepts of using the software and how it works. 

MSC_QuickStart.book (agilent.com)

You said "all possible fragments" - you mean the fragments are theoretical and not observed?  On r/bioinfornmatics I was told that there are multiple precursors with the exact same weight and charge and all of the fragments are lumped into a single precursor reading.  Is that incorrect?

 jamie.dixon ,

What I meant by "all possible fragments" was that any one compound will fragment multiple ways, and that the product ions that are observed cannot necessarily be added together to verify the precursor ion's mass. 

Say for example you have a hypothetical abstract compound A-B-C-D that has a mass of 100. The masses of the individual components are 

A - 10

B - 20

C - 30

D - 40

If this compound had only one way to fragment, say between the B and C, then it would be nice and simple, and your product ion MS/MS spectrum might look something like this.

And the mass of the A-B fragment plus the C-D fragment would equal the precursor ion.

In reality this may be possible, but it is extremely unlikely. Most often there will be multiple ways the molecule can fragment. The product ion MS/MS scan would show signal for each of these fragments, and it is possible that you may not even be able to find each set of pieces that would make the complete ion again.

In this hypothetical example the ion due to just A or just D is not stable and so is not visible in the spectrum.

Regarding your other question, if there are multiple compounds with the same mass and they are not being separated chromatographically then yes, your product ion spectrum will be complicated by the different compounds fragmenting multiple ways all together.

This makes sense.  1 followup question, for that 1st example, (split on A-B, C-D), why does the spectrum show both the A-B value (30), the C-D value(70), AND the A-B-C-D value (100).  Were two fragments analyzed?  Was the same fragment read twice?

jamie.dixon ,

For product ion spectrum you see all fragments generated by an isolated precursor. Depending on the collision cell settings you will typically see some response of the precursor in the product ion scan. Here is an example from some of the demo data that comes with Qual.

The 279 ion was isolated and gives excellent fragmentation data with a fairly low amount of collision energy, so there is still precursor ion signal present. 

This may be a good file for you to investigate and practice with, as it is a very simple example of auto MS/MS data. It can be found on the Qual installation media in the folder Data\Test_PosAutoMSMS.d.

OK - so the original example of just 3 bars: A-B, C-D, A-B-C-D, the A-B-C-D is the precursor and the A-B and C-D are the two fragments.  So the precursor was measured, then split, and the fragments were measure.   And the second bar chart from the prior post - there were multiple precursors all adding to 100, and the fragments split in different ways.  Correct?   I'll check out the test file - thanks!