Sim Score - What is in?

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Loïc Quinton

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Apr 15, 2020, 4:10:24 AM4/15/20
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Dear Diego,

I write an article including XL data analyzed by SIM-XL, and I am trying to understand what is included in the SIM-XL score. I know that scores above 2.5 characterize much probably the best XL matches, even if we have to check the MS/MS spectra manually to confirm it, but how is calculated the score?

For example, does it include mass difference between experimental and theoretical parent ions, number of fragment ions per peptide chain, number of MS/MS spectra characterizing a particular crosslink, intensities, RANSAC analysis... Thanks for the clarification!

Best regards,
Loïc

Paulo C Carvalho

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Apr 15, 2020, 7:34:53 AM4/15/20
to SIM-XL
Dear Loic,

As far as I know, the SIM-XL score is composed of a spectral angle (i.e., a normalized dot product) between the theoretical and the experimental mass spectra plus a reward (I dont recall exactly how much but Diogo can provide the number here), for each peak matched.

All these other tools (RANSAC, ppm precursor versus experimental, etc) are used to draw a final conclusion whether the match is (or not) acceptable.  Matches above 2.5 should be acceptable.

Cheers,
Paulo

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Paulo Costa Carvalho, PhD
Laboratory for Structural and Computational Proteomics
Carlos Chagas Institute, Fiocruz - PR, Brazil
Journal of Proteomics - Executive Editor

Diogo Borges

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Apr 15, 2020, 7:50:03 AM4/15/20
to SIM-XL
Dear Loïc,

SIM-XL score is composed exactly according to what Paulo said. And for each matched peak, a bonus of 0.1 is added to the score. In addition, to try to avoid a bias, a normalization is performed by the length of alpha and beta peptides. 

Best regards,
Diogo

To view this discussion on the web visit https://groups.google.com/d/msgid/simxl/CAOVP5VOdgWoJCAeGoo9vBQUg7ccZcajFZ0rfw3DO%2Bu_6bKd8jg%40mail.gmail.com.

Loïc Quinton

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Apr 16, 2020, 4:22:12 AM4/16/20
to SIM-XL Group
Thank you very much Diogo and Paulo!

All the best,
Loïc

Le mercredi 15 avril 2020 13:50:03 UTC+2, Diogo Borges a écrit :
Dear Loïc,

SIM-XL score is composed exactly according to what Paulo said. And for each matched peak, a bonus of 0.1 is added to the score. In addition, to try to avoid a bias, a normalization is performed by the length of alpha and beta peptides. 

Best regards,
Diogo

Le mer. 15 avr. 2020 à 13:34, Paulo C Carvalho <pa...@pcarvalho.com> a écrit :
Dear Loic,

As far as I know, the SIM-XL score is composed of a spectral angle (i.e., a normalized dot product) between the theoretical and the experimental mass spectra plus a reward (I dont recall exactly how much but Diogo can provide the number here), for each peak matched.

All these other tools (RANSAC, ppm precursor versus experimental, etc) are used to draw a final conclusion whether the match is (or not) acceptable.  Matches above 2.5 should be acceptable.

Cheers,
Paulo

On Wed, Apr 15, 2020 at 5:10 AM Loïc Quinton <loic....@gmail.com> wrote:
Dear Diego,

I write an article including XL data analyzed by SIM-XL, and I am trying to understand what is included in the SIM-XL score. I know that scores above 2.5 characterize much probably the best XL matches, even if we have to check the MS/MS spectra manually to confirm it, but how is calculated the score?

For example, does it include mass difference between experimental and theoretical parent ions, number of fragment ions per peptide chain, number of MS/MS spectra characterizing a particular crosslink, intensities, RANSAC analysis... Thanks for the clarification!

Best regards,
Loïc

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Paulo Costa Carvalho, PhD
Laboratory for Structural and Computational Proteomics
Carlos Chagas Institute, Fiocruz - PR, Brazil
Journal of Proteomics - Executive Editor

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