Previous changeset 3:7e41529ee90c (2013-06-20) Next changeset 5:08bb52273ae1 (2014-02-17) |
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msconvert3.xml msconvert3_raw.xml |
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diff -r 7e41529ee90c -r 001e77708ec9 msconvert3.xml --- a/msconvert3.xml Thu Jun 20 16:08:23 2013 -0400 +++ b/msconvert3.xml Fri Jul 12 12:45:51 2013 -0400 |
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@@ -116,7 +116,7 @@ <!-- BEGIN_VERSION_DEFAULT --> <conditional name="type"> - <param name="input_type" type="select" label="Input Type"> + <param name="input_type" type="select" label="Input Type" help="select file type of input data from history- mzml, mzXML, mgf or ms2. then select appropriate input file from drop down menu depending on input in history"> <option value="mzml">mzML</option> <option value="mzxml">mzXML</option> <option value="mgf">mgf</option> @@ -136,7 +136,7 @@ </when> </conditional> <!-- END_VERSION_DEFAULT --> - <param name="output_type" type="select" label="Output Type"> + <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is The standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)."> <option value="mzML">mzML (indexed)</option> <option value="unindexed_mzML">mzML (unindexed)</option> <option value="mzXML">mzXML (indexed)</option> @@ -145,7 +145,7 @@ <option value="ms2">ms2</option> </param> <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (see also peaklist processing)" /> <when value="false" /> <when value="true"> <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> @@ -363,7 +363,7 @@ <help> **What it does** -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. +Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. You can view the original documentation here_. |
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diff -r 7e41529ee90c -r 001e77708ec9 msconvert3_raw.xml --- a/msconvert3_raw.xml Thu Jun 20 16:08:23 2013 -0400 +++ b/msconvert3_raw.xml Fri Jul 12 12:45:51 2013 -0400 |
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@@ -114,10 +114,10 @@ <inputs> <!-- BEGIN_VERSION_RAW --> - <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> + <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> <!-- END_VERSION_RAW --> - <param name="output_type" type="select" label="Output Type"> + <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)"> <option value="mzML">mzML (indexed)</option> <option value="unindexed_mzML">mzML (unindexed)</option> <option value="mzXML">mzXML (indexed)</option> @@ -126,7 +126,7 @@ <option value="ms2">ms2</option> </param> <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" /> <when value="false" /> <when value="true"> <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> @@ -353,6 +353,21 @@ .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html +**Recommended** + +For X!tandem searches: Use mzml format generated from RAW file. + + RAW → mzml + +For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter. + + RAW → mzml → MGF (ProteinPilot) + +For MaxQuant searches: Use RAW file as an input. + +For OMSSA : Use MGF format generated from mzml file using MGF formatter. + + RAW → mzml → MGF (Mascot) ------ **Citation** |