Re: [Psidev-ms-dev] additional feature request: contiguous/noncontigous marker for m/z array data?

[Darren K. <Dar...@cs...>]

What is the use case for this?

I think everyone has an intuitive understanding of "contiguous", but I  
think it is a little more complicated to define properly.  The  
intuitive definition is "regularly spaced with no missing data points".

When accessing profile data in RAW files from Thermo FT instruments,  
the spectra are thresholded, and this gives rise to the islands that  
Josh mentioned during the conference call.  However, in FT data  
without islands (e.g. if thresholding is disabled, or perhaps with  
preprocessing to extract a single island or fill in missing data  
points), the data points are still not regularly spaced in m/z.  (The  
data points are regularly spaced in frequency space, but the frequency- 
 >m/z calibration function is non-linear).  Because the data points  
are not regularly spaced, any processing must use some form of  
interpolation, so I'm not sure how a "contiguous" flag will help.


Darren



On Apr 16, 2008, at 6:48 AM, Eric Deutsch wrote:

>
> From: Joshua Tasman
>
> Hi all,
>
> There are cases where the m/z array data is contiguous (standard  
> profile
> mode) vs noncontiguous (centroided, or thresholded profile).  Could  
> we add
> an attribute to the binary array section (or above) describing  
> this?  Or is
> this best left to the parsers to automatically determine?
>
> One tricky case that might not be quickly/easily scanned for:  
> imagine a mode
> that preserves profile data points around detected peaks; so the  
> first large
> # of data points might appear to be the same m/z delta.  Hence, a  
> quick
> check by the parser might not get this correct.
>
> Thanks for considering,
>
> Josh
>
>
>
>
>
>
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