[SciPy-user] [half OT?] best way to store a spectrum

Davide Cittaro davide.cittaro@ifom-ieo-campus...
Wed May 27 14:48:42 CDT 2009

On May 27, 2009, at 7:02 PM, Bruce Southey wrote:

> Can you please be more specific?

You're right :-)

> Exactly what do you mean by 'analysis'?

These spectra come from proteomic experiments in which peptides are  
fragmented into ion series which should be matched with theoretical  
spectra (predicted from peptide aminoacidic sequence) to identify  
sequence themselves...

> Do you actually use the intensity values or only those values above a
> set threshold?

:-) In a first attempt I don't think, theoretical spectra are  
difficult to model on intensities. I may use intensity values to get  
only most intense peaks

> What do you really mean by a 'bunch of spectra'?

Thousands or dozen of thousands usually...

> Does each experimental spectrum have a unique corresponding  
> theoretical
> spectrum?


> Do you compare  the 'bunch of spectra' to a single theoretical  
> spectrum?
> Do you compare  the 'bunch of spectra' to a bunch of theoretical  
> spectrum?

I have to find which "theoretical" best matches with an experimental  
(or viceversa)...

> What exactly do you mean by 'match'?

LOL! Sorry if I laugh... scoring a match is a story apart :-)

> To be efficient, you probably want to:
> 1) Vectorize the operations so you want to avoid looping over each
> spectrum. So a single large array may help.
> 2) Find a suitable approach for your analysis as there may be more  
> than
> one approach. Especially getting as many of the calculations as  
> possible
> into lapack functions rather than Python should be faster.
> 3) Try to factoring out constants.


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