Need help using Mascot

Question

[BioStars1993]

I have been given LC-MS/MS data and I am able to perform a search but I'm struggling analyzing the data.

I need to know how to rank identified proteins by expect value and quantify proteins by spectral counts.

I will also need to perferm a G-test and Bonferroni correction so any advice on how to do this would be much appriciated

Thank you in advance!

Answer 1

[Jean-Karim Heriche]

Without more details, it's hard to give you suggestions. Maybe this paper that compares different tests applied to spectral counts will help: Zang et al (2006) Detecting differential and correlated protein expression in label-free shotgun proteomics,” Journal of Proteome Research.

There are also now other methods to estimate protein abundance from spectral counts.

Otherwise, the G-test is a likelihood ratio test, it's not available in R but probably exists in some R packages and there's also code to be found on the net (e.g. the module Statistics::Distributions::GTest for perl)