Hello Jimmy,
I was able to create a .pin file from Comet, but how do I run that in the
external Percolator tool on TPP when it only accepts .txt files? Thank you
for your help!
Best,
Gabby
On Monday, June 8, 2020 at 6:43:54 PM UTC-4, Jimmy Eng wrote:
>
> Confirm that you are using Comet's
Hi Luis,
That worked, thank you so much for your help!
Best,
-Gabby
On Tuesday, June 9, 2020 at 12:29:34 PM UTC-4, Luis wrote:
>
> Hi Gabby,
>
> So since Percolator is not actually running, it just means that the
> interface is confused. On that page where you see the command list, click
>
Thanks @Eric Deutsch , @Phillip Wilmarth
and @Jimmy Eng I will now do the
spectral search using the Spectrast within the TPP toolsuite
On Tue, Jun 9, 2020 at 8:11 PM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:
> Sounds like an XY Problem here.
>
>
>
> If
Hi Srikanth, I suggest after your step “I have convert the results
individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then
apply peptideprophet on each file” (which is good), the next step is merge
the 3 PeptideProphet outputs into a single PepXML file with iProphet. Then
build
Sounds like an XY Problem here.
If it’s spectral clustering you want to do, and within the TPP, perhaps
consider SpectraST:
http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Spectral_Archive_.28Unidentified_Spectral_Library.29_Building
You won’t need to fool around
Hi Gabby,
So since Percolator is not actually running, it just means that the
interface is confused. On that page where you see the command list, click
on "View" (instead of "Kill Job"), and at the bottom of the page that comes
up you will find a small link (at the end of "If your commands have
Hi Javan,
MSConvert can create MS2 format peak lists from RAW files. MS2 format is
kind of a file of concatenated DTA files. It is not too hard to convert
from one to the other. I have probably have a Python script somewhere that
makes MS2 files from folders of DTA files. I am not sure if I
Hello Jimmy,
I have not tried that, that's probably where the problem is coming from. I
will do that and get back to you. Do you know how to kill the command of
the job that is currently running without getting that error? Thank you for
your help!
- Gabby
On Monday, June 8, 2020 at 6:43:54
Hello Luis,
Percolator is no longer running in Task Manager, so it definitely timed
out. I tried to "kill job" in the command page and I keep getting the same
error. Is there a way around this? Thank you for the help.
- Gabby
On Monday, June 8, 2020 at 6:36:45 PM UTC-4, Luis wrote:
>
> Hello,
Thanks all for your help. I now understand why this can't work. The reason
I wanted to use SEQUEST was because the program I wanted to use only takes
.DTA file format for spectral clustering and I have looked around there is
not software which can give me these .DTA file formats.
On Tue, Jun 9,
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