Hey Guys,
I would like to use X!tandem to search phosphopeptide, but I have no idea
how to set other parameters except "residue, potential modification mass".
In other words, I do not know which values is suitable, and I do not find
the item about FDR.
Is default "output, maximum valid expectation value" a little big?
Do you have a set of mature parameters about searching database with
modifications such as phosphorylation?
My main parameters is here, the others follow the default setting. Please
help me to check or modify it.
<note>spectrum parameters</note>
<note type="input" label="spectrum, fragment monoisotopic mass
error">0.02</note>
<note type="input" label="spectrum, parent monoisotopic mass error
plus">10</note>
<note type="input" label="spectrum, parent monoisotopic mass error
minus">10</note>
<note type="input" label="spectrum, fragment monoisotopic mass error
units">Daltons</note>
<note type="input" label="spectrum, parent monoisotopic mass error
units">ppm</note>
<note type="input" label="spectrum, fragment mass
type">monoisotopic</note>
<note>spectrum conditioning parameters</note>
<note type="input" label="spectrum, dynamic range">1000</note>
<note type="input" label="spectrum, total peaks">10</note>
<note type="input" label="spectrum, minimum parent m+h">200.0</note>
<note type="input" label="spectrum, minimum fragment mz">150.0</note>
<note type="input" label="spectrum, minimum peaks">1</note>
<note type="input" label="spectrum, threads">4</note>
<note>residue modification parameters</note>
<note type="input" label="residue, potential modification
mass">79.966@S,79.966@T,79.966@Y</not
<note>model refinement parameters</note>
<note type="input" label="refine">yes</note>
<note type="input" label="refine, use potential modifications for full
refinement">yes</note>
<note>scoring parameters</note>
<note type="input" label="scoring, maximum missed cleavage
sites">2</note>
<note type="input" label="scoring, y ions">yes</note>
<note type="input" label="scoring, b ions">yes</note>
<note type="input" label="scoring, minimum ion count">4</note>
<note type="input" label="scoring, include reverse">yes</note>
<note>output parameters</note>
<note type="input" label="output, maximum valid expectation
value">0.1</note>
Thanks a lot for your future answe!
c qin
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