Hi everyone, I am using the TPP tool tandem2xml for converting X!Tandem results into pepXML.
When using it in command line style for X!Tandem file it went through, but gave multiple error messages as: WARNING: Multiple variable modifications on Q for scan 6605. It only happened for Q (Gln, Glutamine). And only in cases, where Q is the N-terminal amino acid of the peptide. The possible source for the warning message might come from the following fact: - I run X!Tandem with variable modifications - deamidation on N/Q - Furthermore, I allow N-terminal cylization (for N, Q and carbamidomethylated C) in the X!Tandem parameter XML-file, the respective line looks like: <note type="input" label="protein, quick pyrolidone">yes</note> Could possible deamidation at Q and possilbe cylization at N-terminal Q interfere with each other, when converting from X!Tandem.xml output into pepXML-format ? Best, Werner -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
