X!Tandem

[achim.nepaf]

Hiya,

does anybody know, if it is possible to carry out multiple refinement
steps using the X!Tandem interface on Peaks (akin to the "advanced"
form on the gpm interface to X!Tandem,

http://human.thegpm.org/tandem/thegpm_tandem_a.html

This is particularly useful, if one wants to take into account that
one particular amino acid could be modified in two different ways,
e.g. single and double oxidation of M,W or methylation and
carbamidomethylation of K.

Any hints would be very much appreciated,

Achim

[BrianM]

Hi Achim,
While the PEAKS inChorus window for X!Tandem currently does not offer
these advanced features, PEAKS can read the advanced X!Tandem results.
I suggest processing your data using X!Tandem and then import these
results into PEAKS inChorus afterwards for result confirmation.

Cheers,
Brian