Version 6 (modified by b.hoekman@…, 2 years ago)

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Module Settings

Module Properties

Author: bhoekman
Instrument: IonTrap
Data processing step: Feature Quantitation
Program: SuperHirn Feature Quantitation
Version: 0.05 beta

Description

Settings for the SuperHirn program, settings not sorted!!.

Settings

      <Program program="SuperHirn" method="superHirn_peakPicking" format="normal">
            <FileSetReferences>
                <FileRef initialFiles="true" program="" method=""/>
            </FileSetReferences>
            <Parameters>
                <Attribute attributeName="ratiolizer replicate number" value="1"/>
                <Attribute attributeName="MS2 LC retention time resolution" value="0.01"/>
                <Attribute attributeName="static glyco modifictation" value="0"/>
                <Attribute attributeName="min. nb. of profile data points" value="1"/>
                <Attribute attributeName="retention time tolerance" value="0.5"/>
                <Attribute attributeName="max. nb. stripes" value="1"/>
                <Attribute attributeName="FT peak detect MS1 intensity min threshold" value="0"/>
                <Attribute attributeName="Profile Prophet Threshold" value="-1.0"/>
                <Attribute attributeName="Intensity ground level" value="1"/>
                <Attribute attributeName="MS1 feature mz range max" value="1500"/>
                <Attribute attributeName="intensity bin size" value="2000"/>
                <Attribute attributeName="frame inlet" value="50"/>
                <Attribute attributeName="nb. max. alternative protein names" value="5"/>
                <Attribute attributeName="nb. times aligned" value="4"/>
                <Attribute attributeName="intensity end" value="90000000"/>
                <Attribute attributeName="Minimal MS2 fragment intensity value" value="1"/>
                <Attribute attributeName="superHirnRootFileLocation" value="${GALAXY_DATA_INDEX_DIR}/msCompare/SuperHirn/" type="Unknown" description=""/>
                <Attribute attributeName="plot indv. protein ratios" value="1"/>
                <Attribute attributeName="MS1 max inter scan distance" value="10"/>
                <Attribute attributeName="Minimal peak height" value="0.0"/>
                <Attribute attributeName="MS2 info alignment weight" value="0"/>
                <Attribute attributeName="minimal LC/MS score" value="0.1"/>
                <Attribute attributeName="mass start" value="100"/>
                <Attribute attributeName="MS1 intensity apex percentil cutoff" value="0.05"/>
                <Attribute attributeName="ratiolizer probabilty thershold" value="-0.1"/>
                <Attribute attributeName="clustering convergence stopp" value="0.000000000001"/>
                <Attribute attributeName="profile prophet convergence" value="0.00000000000001"/>
                <Attribute attributeName="x end" value="600"/>
                <Attribute attributeName="tr start" value="30"/>
                <Attribute attributeName="Min nb MS2 fragments per consenus spectrum" value="2"/>
                <Attribute attributeName="MS2 intensity apex percentil cutoff" value="0.1"/>
                <Attribute attributeName="store only best MS2 per feature" value="1"/>
                <Attribute attributeName="Report mono peaks" value="1"/>
                <Attribute attributeName="target profile score precentile" value="1"/>
                <Attribute attributeName="LC peak intensity plotting step" value="5000"/>
                <Attribute attributeName="IntensityCV" value="0.9"/>
                <Attribute attributeName="PEPXML DIRECTORY" value=""/>
                <Attribute attributeName="End LC peak score cutoff" value="100000000"/>
                <Attribute attributeName="FT peak detect MS2 min nb peak members" value="1"/>
                <Attribute attributeName="Peptide Prophet Threshold" value="0.9"/>
                <Attribute attributeName="tr end" value="106"/>
                <Attribute attributeName="y end" value="600"/>
                <Attribute attributeName="MASTER MAP PATH" value=""/>
                <Attribute attributeName="MS2 SCAN tolerance" value="100"/>
                <Attribute attributeName="intensity coeff. window" value="3"/>
                <Attribute attributeName="static C-term. modification" value="0"/>
                <Attribute attributeName="LC peak score cutoff" value="1000"/>
                <Attribute attributeName="MS1 LC retention time resolution" value="0.01"/>
                <Attribute attributeName="mz step" value="10.00"/>
                <Attribute attributeName="LC/MS sim. score modus" value="TOTAL"/>
                <Attribute attributeName="Number of histogram plot bins" value="30"/>
                <Attribute attributeName="pairwise correlation analysis" value="0"/>
                <Attribute attributeName="MS1 feature intensity cutoff" value="5000"/>
                <Attribute attributeName="Relative isotope mass precision" value="100"/>
                <Attribute attributeName="Create monoisotopic LC profile" value="1"/>
                <Attribute attributeName="MS1 feature CHRG range min" value="1"/>
                <Attribute attributeName="Min. Replicate Match Number" value="1"/>
                <Attribute attributeName="intensity start" value="0"/>
                <Attribute attributeName="MS1 m/z tolerance" value="1"/>
                <Attribute attributeName="end elution window" value="106.0"/>
                <Attribute attributeName="FT MS2 data centroid data" value="1"/>
                <Attribute attributeName="START LC peak score cutoff" value="0"/>
                <Attribute attributeName="FT monoisotopic toggle correction" value="1"/>
                <Attribute attributeName="similarity matrix" value="0"/>
                <Attribute attributeName="FT peak detect MS2 m/z tolerance" value="0.5"/>
                <Attribute attributeName="print background correction profiles" value="1"/>
                <Attribute attributeName="INCLUSION LIST DIRECTORY" value=""/>
                <Attribute attributeName="MS2 m/z tolerance" value="0.02"/>
                <Attribute attributeName="Report scan number" value="0"/>
                <Attribute attributeName="maximal smoothing error" value="3.0"/>
                <Attribute attributeName="FT MS1 data centroid data" value="0"/>
                <Attribute attributeName="ratio target LC/MS run" value="0"/>
                <Attribute attributeName="INCLUSIONS LIST MS2 SCAN tolerance" value="100000"/>
                <Attribute attributeName="MS1 feature CHRG range max" value="5"/>
                <Attribute attributeName="MASTER alignment plotting" value="1"/>
                <Attribute attributeName="smoothing error TR window" value="1"/>
                <Attribute attributeName="pairwise alignment plotting" value="1"/>
                <Attribute attributeName="Absolute isotope mass precision" value="0.3"/>
                <Attribute attributeName="MS2 mass type check" value="0"/>
                <Attribute attributeName="gauss data percentile" value="0.95"/>
                <Attribute attributeName="Target Profile Scoring" value="1"/>
                <Attribute attributeName="size titel" value="20"/>
                <Attribute attributeName="Centroid window width" value="5"/>
                <Attribute attributeName="Peptide Proteotype Mode" value="1"/>
                <Attribute attributeName="global cluster modus" value="0"/>
                <Attribute attributeName="profile prophet maximal iterations" value="500"/>
                <Attribute attributeName="MS2 fragment mass tracing" value="0"/>
                <Attribute attributeName="FT peak detect MS1 min nb peak members" value="4"/>
                <Attribute attributeName="N-th highest fragment in MS2 spectrum" value="2"/>
                <Attribute attributeName="min. nb. of cluster members" value="100"/>
                <Attribute attributeName="Tryptic peptide selection" value="0"/>
                <Attribute attributeName="Delta pair TR tolerance" value="-1"/>
                <Attribute attributeName="MS2 max inter scan trace distance" value="500"/>
                <Attribute attributeName="tr step" value="5.00"/>
                <Attribute attributeName="number of clusters" value="0"/>
                <Attribute attributeName="mass / charge window" value="1"/>
                <Attribute attributeName="MS1 retention time tolerance" value="0.5"/>
                <Attribute attributeName="MS2 mass matching modus" value="1"/>
                <Attribute attributeName="store only best MS2 per ALIGNED feature" value="1"/>
                <Attribute attributeName="retention time window" value="5.0"/>
                <Attribute attributeName="MS1 feature mz range min" value="100"/>
                <Attribute attributeName="start elution window" value="15.0"/>
                <Attribute attributeName="Min. number histo data points" value="60"/>
                <Attribute attributeName="perc. outside error delta points" value="0.75"/>
                <Attribute attributeName="gnuplot plot generator" value="1"/>
                <Attribute attributeName="TIC integration over peptide modification variants" value="0"/>
                <Attribute attributeName="Detectable isotope factor" value="0.2"/>
                <Attribute attributeName="target profile clustering initiation" value="0"/>
                <Attribute attributeName="print alignment tree" value="0"/>
                <Attribute attributeName="transformationFileLocation" value="${GALAXY_DATA_INDEX_DIR}/msCompare/settings/transformations/featureListTransformations.xml"/>
                <Attribute attributeName="LC peak intensity cutoff" value="0"/>
                <Attribute attributeName="MS2 Delta clustering filter" value="0"/>
                <Attribute attributeName="MS2 retention time tolerance" value="-1"/>
                <Attribute attributeName="MS1 feature plot dot size" value="5"/>
                <Attribute attributeName="Debug directory" value=""/>
                <Attribute attributeName="intensity bin tolerance" value="2"/>
                <Attribute attributeName="MS2 feature plot rec size" value="6"/>
                <Attribute attributeName="ratiolizer replicate check" value="1"/>
                <Attribute attributeName="normalization feature align percentage" value="1.0"/>
                <Attribute attributeName="FEATURE COLOR MODE" value="3"/>
                <Attribute attributeName="retention time step" value="1.0"/>
                <Attribute attributeName="FT peak detect MS1 m/z tolerance" value="1"/>
                <Attribute attributeName="mass end" value="1500"/>
                <Attribute attributeName="size text" value="16"/>
                <Attribute attributeName="FT peak detect MS2 intensity min threshold" value="10"/>
                <Attribute attributeName="End LC peak intensity cutoff" value="50000"/>
                <Attribute attributeName="max. nb. of iterations" value="1000"/>
            </Parameters>
        </Program>