How to set values for each parameters?

[Timsy singh]

Hello,
greetings!

Thank you very much for your video and the reply to visit this site. I am using this software for the first time to analyze my master thesis results. I have two set of treatments/ samples: Mock and Pseudomonas treated.  I want to look/compare  the metabolites produced in " Mock" treated plants and in Pseudomonas treated plants.

I tried using this software, but I think hardly know anything about it . I face troubles each time when I need to put parameters such as following:

1. m/z tolerance : How to decide m/z tolerance for steps like Chromatogram builder/ Peak Normalization/ Alignement and so on.
I am using the same value as given in manual( 0.02 -5.0)

2. m/z or RT tolerance : How to decide or what are the bases of deceiding m/z weight or RT weight in"Alignement step"? How should I know what is this? "Help" option does not help me either. I used the same as in manual. DO NOT know how correct I am doing.

3. Noise level or Baseline: Is Noise level or baseline same thing? Secondly, How to choose/ decide this? What I understood from "Help", it is the minimum height of the peak below which every other peaks would not be counted. Keeping this in mind, I chose that peak from base peak chromatogram, which shows m/z labeling and is smallest among all the peaks which are labelled with m/z on them. Is this correct way to choose it?

I have attached the Base peak chromatogram for you to better understand what I am asking. I chose a value of 1.2E5 as noise level( marked in image) and the height of the smallest peak and used this everywhere whenever I was asked to put either absolute min height or noise level or min standard intensity etc.


Overall, Please help me understand how to decide the values to fill in parameter box under each step till  PCA and log ratio step.

I know this is so much I am asking you, but believe me I a student a biology who never dealth with physics and softwares like this and on top of that Nobody in my deptt knows how to work with this software not even my supervisor under whom I am working.

Thank you so much for your kind understanding and quick reply.
Looking forward to your answer!

Best regards,
Timsy

[Tomas Pluskal]

Hi Timsy,

You should use the integrated previews to observe the effect of the
different parameter values. Also take a close look at your raw data.
The m/z tolerance should be set such that it covers the m/z accuracy
range of your instrument (how much your m/z signals deviate in
consecutive scans?). The RT tolerance depends on the reproducibility
of your chromatography - again, observe your raw data to optimize the
values. You will never obtain good results if you just copy values
from manual, you need to first understand what the values mean.

Best,

Tomas

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