Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
On Mar 3, 5:16 pm, Jimmy Eng jke...@gmail.com wrote:
unless there's a way to convert .msf to pep.xml, and I'm not aware of
any tool that does this, you'll have to go the .out route.
On Mar 3,
You should search your Proteome Discoverer box for a file named
'sequest.params' as I don't have access to the Thermo version. In
fact, I wouldn't even know if sequest.params still exists under
Discoverer.
Here's the current params file we use at the UW (which is similar to
but not directly the
Dear All:
I tried to use TPP to analyze the SILAC data produced from Velo under Xcaliber
2.1. The sequest results for each fraction is very big and I have total 30
fraction. I tried ONE fraction with TPP and it is fine to convert the raw data
into mzxml and sequest results to pepxml. When I try
I try to use TPP to analyze the SILAC results, which is from Velo (Xcalibar :
2.1). The result files (total 30 fraction files) are really big (14G after
zipped). I tested one fraction with TPP and it can transfer to mzxml and pepxml
after I install Xcalibar 2.1. When I tried to load more such
No params file it is set in either workflow or standalone sequest
que. They are dropdowns to choose pre-populated mods (variable and
static). So doing the mods is easy. I can send ex. workflow but if
you are using PD you would see these readily.
Converter for msf would be tough but the app
I can drop off examples of export options if someone else want s to
have a look see. I will also discuss w/ Thermo to see if there is
something they can do on their end quickly.
On Mar 4, 7:08 pm, Jimmy Eng jke...@gmail.com wrote:
You should search your Proteome Discoverer box for a file named
When I run from Discoverer, it asked me to select all the options and
generated a template which can be used later. As I search the
computer, no sequest.params files exists. But if I run sequest.exe
from
command line, it asks for sequest.params file.
I tried the params file you attached, it seems
Thanks for the response.
I find the function to export prot.xml, but the probability there is
not peptide
prophet, right?
We need peptide prophet from the sequest search, and thus we can
make comparison with other search results which are measured by
peptide
prophet.
On Mar 4, 5:39 pm, DD
