Hello Zack,
Each evaluated modification site gets a PTMProphet calculated probability
of the modification being at that site. If you mouse over the bar you will
get the value of the probability. You can export the results to xls file
and the ptm_peptide column will show the values next to the ev
Hi David,
Thanks for posting the path to the PTMProphet documentation--was just
looking for it last night.
After analyzing some data, and when viewing it in the PepXML viewer, what
is the significance of the colored boxes above the individual residues in
the PTMPeptide column? Despite the docu
Hi Paul,
It sounds like what you are looking for is the MASSDIFFMODE option in
PTMProphet. You can run MASSDIFFMODE on MSFragger results and it will
localize the mass difference of each ID like a PTM. You should set MZTOL=
parameter to be consistent with the mass accuracy of your dataset on the
Brian and David,
Thank you for chiming in. Yes, I am aware of the "--help" option that is
available. I was hoping to get a better understanding of PTMprophet in
particular, so thank you for highlighting the upcoming publication. In
regards to PTMProphet, I'd like to use this in conjunction with
I accidentally posted this twice. Topic has been addressed in earlier post.
On Friday, January 5, 2018 at 1:44:54 PM UTC-5, Paul Abraham wrote:
>
> Hello,
>
> It seems that the wiki page has very limited information on how to most
> efficiently use the TPP tools. For example, the tool PTMProphet
Hello,
It seems that the wiki page has very limited information on how to most
efficiently use the TPP tools. For example, the tool PTMProphet is listed
as a tool yet doesn't have any documentation. It is quite frustrating when
you have to mine google group forums to identify what didn't work f
Hello Paul,
You can get the instructions on using PTMProphet by running the tool on the
commandline without any options. This applies to most of the commandline
tools in the TPP.
When you type "*PTMProphetParser" *into the commandline, you'll get the
following usage statement:
*P
Hello Paul,
The quickest way to greater understanding on the use of the tools is to execute
the binaries in question at the command line with no options specified. The
output will show information about their usage. For example on my old Linux
install of TPP 4.8, at the command line, I change
Hello,
I am having a difficult time locating documentation for several of the TPP
tools. For example, the PTMProphet tool referenced on the wiki page does
not have any supporting documentation. Am I missing some obscure landing
page somewhere? The only information I find for how to efficiently
