PDV
PDV: an integrative proteomics data viewer
Install / Use
/learn @wenbostar/PDVREADME
PDV: an integrative proteomics data viewer
PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets in different formats on standard desktop computers in both graphical user interface and command line modes. One of the most important functions of PDV is to visualize peptide identification results from different search engines and generate high quality annotated spectra for publication.
Usage
A user's manual is available at http://pdv.zhang-lab.org. You can find some visualization examples in the user's manual or the manuscript of PDV.
Installation
The PDV package can be downloaded at https://github.com/wenbostar/PDV/releases.
Example
MSFragger-Glyco
PDV supports visualizing N-linked intact glycopeptide identification result (identification file: psm.tsv, MS/MS file: mzML format) generated by MSFragger-Glyco/Philosopher. An example input can be downloaded at MSFragger-Glyco_example.
<img src="http://pdv.zhang-lab.org/data/download/glyco.png" width=600 class="center">USI (Universal Spectrum Identifier)
<img src="http://pdv.zhang-lab.org/data/download/PDV_USI_example.jpeg" width=600 class="center">
Mirror plot (Experimental spectrum VS predicted spectrum using deep learning)
Top panel: experimental spectrum, bottom panel: predicted spectrum using deep learning.
<img src="https://github.com/wenbostar/PDV/assets/5302110/bbf49a24-5a68-41f4-85a0-1091e0013d7b" width=600 class="center">Database searching:
| Software | Example files | | ----------------|:---------------| | PepQuery | PepQuery | | MS-GF+ (v2017.01.13)| mgf:mzid<br>mzML:mzid<br>mzXML:mzid| | X!Tandem (v2017.2.1.2) | mgf:mzid (convert X!Tandem XML result to mzid file using MzidLib)| | MyriMatch (v2.2.10165) | mgf:mzid<br>mgf:pepXML<br>mzML:mzid<br>mzML:pepXML<br>mzXML:mzid<br>mzXML:pepXML | | Comet (v2018.01 rev. 2) | mgf:pepXML<br>mzML:pepXML<br>mzXML:pepXML | | Crux/Tide (v3.2)| mgf:pepXML<br> mgf:mzid<br>mzML:pepXML<br>mzML:mzid<br>mzXML:pepXML<br>mzXML:mzid | | Crux/Tide (v4.1)| mzML:pepXML<br>mzML:mzid<br>mzXML:pepXML<br>mzXML:mzid | | MS Amanda (v2.0.0.11219) | mgf:csv(MS Amanda format)<br>mzML:csv(MS Amanda format) | | MSFragger (v20180316) | mzML:pepXML<br>mzXML:pepXML| | FragPipe | Manual | | MaxQuant | version 1.3.0.5<br>version 1.5.3.30<br>version 1.5.4.1<br>[version 1.5.7.4](http://
