Hi Ira,
Without looking at the code, I recall that Mascot2XML depends on certain title formats. Msconvert
preserved the Bruker nativeID of scan=xxx which is not one of those formats.
This is a good reason to have user-customizable MGF titles in pwiz (and thus msconvert). I think a
TPP
Hi-
I just downloaded the latest version of TPP this week, so version:
TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW)
I'm still really hoping for an answer for the -Etrypsin error.I'm
stuck until I get that figured out.
Thanks!!
Ruby
On Feb 28, 12:04 pm, Joe Slagel
Ruby,
The problem likely has nothing to do with the -Etrypsin option in the
Out2XML command. Do you have a bunch of *.out files in the directory
c:\Inetpub\wwwroot\ISB\data\RG_81_2\
Are those files named something like RG_81_2.1.1.1.out?
- Jimmy
On Tue, Mar 1, 2011 at 1:58 PM,
Thanks for the reply, Matt.
Ira: in the meantime, you can either write a script that will insert
TPP-style TITLE headings to your mgf files (pre-Mascot), or convert your raw
data to mzXML, followed by mgf using mzXML2Search.
For full TPP compatibility, you will also want to rename the Mascot.dat
Hi Jimmy-
The directory does have the .out files (as that is what I thought I
needed to use for the pepXML conversion). Please correct me if I'm
wrong...
I just looked through several of the data directories that I have
tried and received this error for, and I don't have any files with the
Hi Ruby,
A couple of more things on top of what Jimmy just posted:
1) While probably not the reason your conversion is failing, there is a way
to specify a semi-enzyme search when converting to pepXML: you want to use
-Esemitrypsin as a parameter to Out2XML. Unfortunately, that option is not
