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compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
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Could moFF output the retention time boundary of the integrated ion intensity envelop #9

Closed fcyu closed 7 years ago

fcyu commented 7 years ago

I know that moFF output "lwhm" and "rwhm". However, they are not the boundary. Could moFF output the boundary for us to plot the curve easily?

Thanks

Maux82 commented 7 years ago

Hi,

Can you explain me with more details the time boundary that you need ? In principle you can get the entire XiC inside the intervall rt +/- rt_w.

fcyu commented 7 years ago

Hi,

Thanks for your reply. I would like to illustrate it with a figure:

681689538615036753

I marked the left boundary and right boundary with red color. It is clear that only the intensities within this range should be integrated. moFF reports LWHM and RWHM which are narrower than left boundary and right boundary. Thus, I wonder if moFF could report two boundaries?

Thanks

Maux82 commented 7 years ago

Hi ,

Sorry for my late reply but I was on holiday. Yes of course, it is possible to detect the rt boundary of the peak but to do that you need to consider the peak intensities as peak area considering the isotopic envelope of the possible peptides. This is the opposite of the apex approach of moFF that aims to keep away the computatioanl burden of the intensities integration.

At the moment this feature is not the list of the next moFF improvements, but of course you are really welcome to implement it by your own starting from the moFF code.

fcyu commented 7 years ago

Hi,

Thanks for your reply.

Now, I am confused. I recheck your paper, there is no details about how to get the total ion intensity after obtaining the apex. Could you please briefly describe the algorithm since it is not based on the intensities integration?

Thanks

Maux82 commented 7 years ago

moFF, for every features both for machted or ms2 identified, extracts the apex intensitiy in the XiC related to the monoisotopic mass of the feature (using the rt_w, and the rt_p windows). In moFF there is no any kind of intensities integration, it provides only apex intensities.

Here, you can find a slide that explains how the apex is extracted and how the quality metrics are computed.

fcyu commented 7 years ago

Thanks for your clearly reply.