Of course, I am glad to help. The old and the new versions should run
faster on the centroided data. There is no way to tell *a priori* with
ASAPRatio how long it will take, but since it ran to completion on my
machine and it generates one dot per ten PSMs it has processed; based on
the dots you
Thank you so much David for doing this for me. In fact I was running
asapratio again on the centroid mzml file. But I see that though express
completed easily but the asapratio is still running. Is there any way in
tpp to see how much time will it take to complete.
But I will try with the version
Hello Sudarshan, again!
I was able to update the ASAPRatioPeptideParser.exe tool for your testing
purposes to see if it runs a bit faster after some optimization I was able
to implement. Please download the following version:
Hopefully, I am understanding your queries correctly, here goes.
Centroiding the data will reduce the number of peaks in the spectra and
reduce the running time of the analysis. Compressing the files to make
them smaller will require that the tools reading the files uncompress the
data (usually
one more query-
I used same samples - for label free and SILAC express?
Ideally I should get a similar conclusion from both the experiments.
But the differentially expressed proteins are different in the two analyses.
NOte: I have used only one run file of control and one run file of
treatment
Hi David,
I am using this tutorial for Expressan dASAPratio . can yuo please
comment on if I am using the right one.?
Regards,
Sud
On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar
wrote:
> can i select all the three options?
> Will it impact Express analysis?
> Centroid all scans (MS1 and MS2)
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,
Thank you so much . I will try the way have suggested.
Best regards
Sud
On Wed, Nov 29, 2023, 1:37 PM David Shteynberg <
dshteynb...@systemsbiology.org> wrote:
> Dear Sud,
>
> I was able to process your dataset! Although, I am still working on
> getting a faster version of ASAPRatio compiled
Dear Sud,
I was able to process your dataset! Although, I am still working on getting a
faster version of ASAPRatio compiled for your testing purposes. Meanwhile you
can help the process by filtering your files so that zero intensity peaks in
the MS1 data are removed and the MS1 data is
