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<div class="title">ConvertTSVToTraML </div> </div>
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<div class="textblock"><p>Converts OpenSWATH transition TSV files to TraML files</p>
<p>The OpenSWATH transition TSV files need to have the following headers, all fields need to be separated by tabs:</p>
<ul>
<li>
PrecursorMz (float) </li>
<li>
ProductMz (float) </li>
<li>
Tr_calibrated (float) </li>
<li>
transition_name (free text, needs to be unique for each transition [in this file]) </li>
<li>
Collision Energy (float) </li>
<li>
LibraryIntensity (float) </li>
<li>
transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) </li>
<li>
decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) </li>
<li>
PeptideSequence (free text, sequence only (no modifications) ) </li>
<li>
ProteinName (free text) </li>
<li>
Annotation (free text, e.g. y7) </li>
<li>
FullUniModPeptideName (free text, should contain modifications*) </li>
<li>
PrecursorCharge (integer, contains the charge of the precursor) </li>
<li>
GroupLabel (free text, e.g. heavy or light) </li>
<li>
UniprotID (free text) </li>
<li>
FragmentType (free text, contains the type of the fragment, e.g. "b" or "y") </li>
<li>
FragmentCharge (integer, contains the fragment charge) </li>
<li>
FragmentSeriesNumber (integer, e.g. for y7 use "7" here) </li>
</ul>
<p>modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS. Please do not use the ambiguous bracket notation (e.g. PEPT[+80]IDE or PEPT[181]IDE) since this is ambiguous and will NOT be interpreted correctly! example: PEPT(Phosphorylation)IDE(UniMod:27)A ) </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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