Re: [spctools-discuss] Re: EXpress in SILAC

2023-11-30 Thread Jimmy Eng
I thought I did. Here's what I wrote regarding XPRESS: It simply reports light area to heavy area ratios. You'll have to do adjustments after the fact i.e. centering the mean ratio to 1:1 if you expect the bulk of your samples to be 1:1. If that doesn't answer your normalization question,

Re: [spctools-discuss] Re: EXpress in SILAC

2023-11-30 Thread sudarshan kumar
Hi Jimmy, Can you please explain my query. Regards, Sud On Wed, Nov 22, 2023 at 3:13 PM sudarshan kumar wrote: > Oh ! thank you > Let me explain- > I have mixed two samples light and heavy labelled proteins (at cell level) > But if the cell count was not equal in the two groups, it will result

Re: [spctools-discuss] running ASAPratio for SILAC data

2023-11-30 Thread sudarshan kumar
can i select all the three options? Will it impact Express analysis? Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired in profile mode Compress peak lists for smaller output file Write the output as a gzipped file (other TPP tools can read gzipped files directly) On Wed,