Sugandima Vidanagamachchi

4 Questions 11 Answers 0 Followers

Questions related from Sugandima Vidanagamachchi

What should be the parameter settings for default_input.xml file in X!Tandem for 4-plex iTRAQ?

I have used the X!tandem software for proteomics data search and couldn't get the correct output for my current settings below. Residue modifications-> 144.1021@K Residue potential...

03 March 2015 6,522 7 View

Why do I miss H/L ratio in MaxQuant output?

I used SILAC experiment data (labeled) in MaxQuant and it doesn't include the standard. In MaxQuant I didn't get H/L ratio. How can I quantify the proteins with these conditions? Thank you.

02 February 2015 7,582 5 View

Is there any way of identifying proteins/peptides with a MS peaklist in R?

I have a set of MS data and I used a function mzPick() in R to find the peak list. Then I wrote the peak list to a file and it outputs the mean values of m/z of peak measurements and variations of...

01 January 2015 755 6 View

What are the steps of finding detectability of a peptide in a given protein mixture?

If I have a peptide set identified from mascot search tool, how can I find and use detectability of peptides for better inference of proteins?

07 July 2014 8,737 1 View