Created
January 17, 2017 08:59
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OpenMS workflow, peptide feature detection, Sciex TripleTOF 6600 (centroid mode), 9/01/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="3" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="2" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| <LISTITEM value="../../PeptideQuantification_SciexTripleTOF6600_centroided/commandline/Yasset Perez-Riverol - 140702_0002_DC2ac_6600_G2_DDA1-DC2ac_6600_G2_DDA1.mzML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-280" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FeatureFinderMultiplex" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-120" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="LC-MS dataset in centroid or profile mode" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="output-file" description="Optional output file containing the individual peptide features in 'out'." required="false" advanced="true" supported_formats="*.featureXML" /> | |
| <ITEM name="out_mzq" value="" type="output-file" description="Optional output file of MzQuantML." required="false" advanced="true" supported_formats="*.mzq" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="labels" value="" type="string" description="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10] ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC#br#[Dimethyl0][Dimethyl6] ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL" required="false" advanced="false" /> | |
| <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." required="false" advanced="false" /> | |
| <ITEM name="isotopes_per_peptide" value="3:5" type="string" description="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " required="false" advanced="true" /> | |
| <ITEM name="rt_typical" value="50" type="double" description="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_min" value="10" type="double" description="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="10" type="double" description="m/z tolerance for search of peak patterns." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_unit" value="ppm" type="string" description="Unit of the 'mz_tolerance' parameter." required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="intensity_cutoff" value="10" type="double" description="Lower bound for the intensity of isotopic peaks." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide_similarity" value="0.9" type="double" description="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity" value="0.8" type="double" description="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity_scaling" value="0.75" type="double" description="Let x denote this scaling factor, and p the averagine similarity parameter. For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)" required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="knock_out" value="false" type="string" description="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="averagine_type" value="peptide" type="string" description="The type of averagine to use, currently RNA, DNA or peptide" required="false" advanced="true" restrictions="peptide,RNA,DNA" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'algorithm:labels'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="double" description="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="double" description="Label:2H(4) | H(-4) 2H(4) | unimod #481" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="double" description="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Leu3" value="3.01883" type="double" description="Label:2H(3) | H(-3) 2H(3) | unimod #262" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl0" value="28.0313" type="double" description="Dimethyl | H(4) C(2) | unimod #36" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl4" value="32.056407" type="double" description="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl6" value="34.063117" type="double" description="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl8" value="36.07567" type="double" description="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL0" value="105.021464" type="double" description="ICPL | H(3) C(6) N O | unimod #365" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL4" value="109.046571" type="double" description="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL6" value="111.041593" type="double" description="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL10" value="115.0667" type="double" description="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-300" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/1" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/2" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out_features" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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