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Added FragPipe result visualization manual
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wenbostar authored Nov 26, 2023
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Expand Up @@ -44,7 +44,7 @@ PDV supports visualizing N-linked intact glycopeptide identification result (ide
| [Crux/Tide](http://crux.ms/) (v4.1)| [mzML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/crux_4.1/crux-output_mzml/tide-search.target.pep.xml.gz)<br>[mzML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz):[mzid](http://pdv.zhang-lab.org/data/download/test_data/crux_4.1/crux-output_mzml/tide-search.target.mzid.gz)<br>[mzXML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzXML.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/crux_4.1/crux-output_mzxml/tide-search.target.pep.xml.gz)<br>[mzXML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzXML.gz):[mzid](http://pdv.zhang-lab.org/data/download/test_data/crux_4.1/crux-output_mzxml/tide-search.target.mzid.gz) |
| [MS Amanda](http://ms.imp.ac.at/index.php?action=ms-amanda) (v2.0.0.11219) | [mgf](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf.gz):[csv](http://pdv.zhang-lab.org/data/download/test_data/msamanda/SF_200217_U2OS_TiO2_HCD_OT_rep1_MSAmanda_mgf.csv.gz)(MS Amanda format)<br>[mzML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz):[csv](http://pdv.zhang-lab.org/data/download/test_data/msamanda/SF_200217_U2OS_TiO2_HCD_OT_rep1_MSAmanda_mzML.csv.gz)(MS Amanda format) |
| [MSFragger](https://www.nature.com/articles/nmeth.4256) (v20180316) | [mzML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/msfragger/SF_200217_U2OS_TiO2_HCD_OT_rep1_msfragger_mzML.pepXML.gz)<br>[mzXML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzXML.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/msfragger/SF_200217_U2OS_TiO2_HCD_OT_rep1_msfragger_mzXML.pepXML.gz)|
| [FragPipe](https://github.com/Nesvilab/philosopher/) | Fully supported |
| [FragPipe](https://github.com/Nesvilab/philosopher/) | [Manual](https://github.com/wenbostar/PDV/wiki/Visualize-FragPipe-result) |
| [MaxQuant](http://www.coxdocs.org/doku.php?id=maxquant:start) | [version 1.3.0.5](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.3.0.5.tar.gz)<br>[version 1.5.3.30](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.5.3.30.tar.gz)<br>[version 1.5.4.1](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.5.4.1.tar.gz)<br>[version 1.5.7.4](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.5.7.4.tar.gz)<br>[version 1.5.8.3](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.5.8.3.tar.gz)<br>[version 1.6.2.3](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.6.2.3.tar.gz)<br>[version 1.6.5.0](http://pdv.zhang-lab.org/data/download/test_data/maxquant/maxquant_1.6.5.0.tar.gz) |
| [IPeak](https://www.ncbi.nlm.nih.gov/pubmed/25951428)| [mgf](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf.gz):[mzid](http://pdv.zhang-lab.org/data/download/test_data/ipeak/SF_200217_U2OS_TiO2_HCD_OT_rep1_IPeak_mgf.mzid.gz) |
| [IdentiPy](https://bitbucket.org/levitsky/identipy) (v0.2)|[mgf](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/identipy/SF_200217_U2OS_TiO2_HCD_OT_rep1_identipy_mgf.pep.xml.gz)<br>[mzML](http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz):[pepXML](http://pdv.zhang-lab.org/data/download/test_data/identipy/SF_200217_U2OS_TiO2_HCD_OT_rep1_identipy_mzML.pep.xml.gz)|
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