I'm analyzing a dataset with Amdis. It's a big set of unknown samples ran in the same conditions, so my strategy is to match compounds across samples mainly based on the RT.
I started by setting the analysis parameters to be rather permissive with regards to the MS match (50 min match factor) but strict regarding RT (RT window of 0.2 min, strong level penalty and 70 max penalty).
The logic is that I don't expect large RT shifts between samples, so I want to identify any compound which runs at the same time and is structurally similar to my target compound.
The problem is that Amdis seems to penalize components for no reason. For example, I have a component running at 3.766 min which is structurally very similar (weighted match - 99 and 98) to two components in the library whose expected RTs are 3.763 and 4.128.
I would like Amdis to associate the component only with the first target (RT diff 0.003) and expected the latter to be heavily penalized for the 0.36 min difference. However, both got exactly the same RETENTION penalty of -20.
Screen capture:
https://drive.google.com/file/d/0B7RthaJaJIzxRnhTb1lBbnlHU2M/view?usp=sharing
Is this a bug? Or am I missing something?
https://drive.google.com/file/d/0B7RthaJaJIzxRnhTb1lBbnlHU2M/view?usp=sharing
What I see from the picture is, that in both cases the penalty is -20, which therefore might be the maximum penalty (different to your statement of -70). Also your first substance, that has nearly perfect retention time, gets the maximum penalty.
What is your RI window (see attached picture), which defines your interval without penalty?
The AMDIS help file explains quite good, how this RI penalties are calculated.
Thanks for the reply.
I double-checked and the max penalty is 70, so I'm not sure where the 20 comes from.
Further, I can now confirm that analyzing using the "strong" match factor penalty, changing to "very strong", analyzing and then back to "strong" solves the problem - the component is associated only with the correct target and no penalty is applied.
This strongly implies that it's a bug.
I didn't run the analysis with RI's, and as far as I understand if I run an analysis using "use retention time", parameters for the RI analysis are not used at all. Am I wrong?
You are right, the RI parameters are not used when you use the retention time analysis in AMDIS.
I never ran into this problem using Retention Indices.
BTW, I would strongly advice to ALWAYS use Retention Indices when using AMDIS even if you don't expect RT shifts. Within a sequence using RT's won't be a big problem, but what if you want to do more experiments in a couple of weeks
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