bump
Can someone please describe how ProteinProphet employs I-L exchange?
thanks
On Sep 7, 11:22 am, John Damask jbdam...@gmail.com wrote:
Hi,
We're running TPP v4.3 rev1 and I have a question about
ProteinProphet. We just ran into a case where an I-L exchange in a
peptide made the
Here is what I did. I generate a mzXML from Thermo RAW data using
ReAdW. Then I ran msconvert to try to get a mgf file from that mzXML
generated from RAW data (The command was: msconvert --.mzXML --.mgf;
also tried other ways like: msconvert --.mgf --.mzXML etc). But the
software always generate a
Dear list,
I have three question regarding ASAP and XPRESS:
1)
I analyzed a data set generated from a SILAC sample on an Orbitrap.
The data was searched using Sequest with variable modifications on R
and K. I used ASAP and XPRESS for quantitaton with the following
command (TPP v4.3 JETSTREAM rev
Lukas,
These tools could definitely be optimized and improved, especially for
high res data that didn't really exist when they were first developed.
That said, with respect to question 1, you're using two imperfect
tools on presumably large datasets so it's not surprising to see some
Dear Jimmy,
thanks for your quick answer. I will for sure look into the raw data
and hope to see a trend which is the reason for this effect.
What I forgot to mention in the post before, is that I post filtered
the results with a very stringent PPS cutoff of 0.99. So the reason
cannot be false
