Peak renumbering?

Analysis Version 3
1

Hi everyone,

I’m wondering if it is possible to renumber Peaks in the PeakList in V3 for Windows 10. I have two issues regarding this. The first is that, once I use the automated Peak Picker on a 2D spectrum, I often find several peaks picked are noise (I’m looking at a protein + dose titration of small molecule). When I go to delete them–for example, peak 210–the subsequent peaks are not renumbered, so my list goes 208, 209, 211, etc. This makes it difficult to easily see how many peaks are in a spectrum. Secondly, if I use the automated peak picker but then realize I forgot to change the minimum for the H axis, I’ll undo peak picking and then perform it again with the proper minimum. However, all of the peaks continue numbering as though I kept the first set. For example, if I have 250 peaks picked the first time and click undo, the next peak pick creates a table that starts at 251. The only way I’ve gotten around this second issue is to delete the spectrum and re-open it, which is tedious.

Is there a solution to this? Am I focusing on something that isn’t important?

Thanks!

1 Like
2

I also encountered these issues and look forward to solutions or guidance. :saluting_face:

1 Like
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Dear Ken and Nix

Overview

There is method in the madness here! Explanations below but first off the simplest answer is the easiest way to renumber all the peaks is to copy them into a new list and delete the old one (see how to clone a peak list below for more details on how to do this correctly). However, as described below this has consequences if you have used your peak numbers elsewhere

Explanation

So why the strange behaviour that I can’t have peaks numbered the way I want (I am possibly partially responsible for this, it was feature I suggested for `NMRView many years ago and which got adopted by CCPN for good reason, though I am sure others came up with similar ideas in parallel).

So the problem is if you use peak numbers to record something about a spectrum (say a nOes for a structure calculation) you can quite quickly run into a situation as follows where things are inconsistent and confusing

Lets define some peaks

  1. 1.00ppm - 130.00ppm
  2. 4.00ppm - 135.00ppm
  3. 5.00ppm - 140.00ppm

Now I run them through a program and peak 2. Comes back as violated

But at the same time I have done some more work on the spectra and peak list and decided that 2. Is a rubbish peak* so now I have

  1. 1.00ppm - 130.00ppm

  2. 5.00ppm - 140.00ppm

But then I add a new peak, if we reused peaks we can end up with something like this

  1. 1.00ppm - 130.00ppm
  2. 5.50ppm - 145.00ppm
  3. 5.00ppm - 140.00ppm

Now I am sitting scratching my head as to why the lovely peak I now have at 5.50ppm and 145ppm is violated by my structure calculation. However, if we don’t reuse peak numbers we now have

  1. 1.00ppm - 130.00ppm

  2. 5.00ppm - 140.00ppm

  3. 5.50ppm - 145.00ppm

Which is a lot more obvious as since 2 is deleted I assume it was a bad peak and there is less confusion and error

How to clone a peak list

  1. Use the menu Spectrum->Copy Peak list
  2. In target spectra right click and select remove all
  3. In the drop down select the name spectrum as you are copying the peak list from
  4. Select the radio button copy all existing properties
  • of course this could all happen over a period of weeks, how good is your memory across 1000s of peaksand long periods of time ;-)

I hope that helps

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:telephone::01227 82 7117
:envelope:: g.s.thompson@kent.ac.uk
orchid: ORCID

1 Like
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Thanks for your answer. Now I know the reasons and the appropriate approach for handling my peak list numbering.

regards
Ken

5

Hi Dr. Thompson,

Thanks so much for your detailed explanation! This is very insightful. Is there a way to quickly total the true number of peaks on a spectrum regardless of numbering? By copying them into a new list as described?

Much appreciated,
Nix

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At the moment select all the peaks in the list either on the spectrum or using a peak. V
List module (control a for select all should work) then double space bar to get the console and type len(current.peaks) we should add a count at the top of the peak list modules as a feature