PDV is a JAVA tool for proteomics data visualization.
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.
The PDV package can be downloaded at https://github.com/wenbostar/PDV/releases.
| Software | Example files |
|---|---|
| MS-GF+ (v2017.01.13) | mgf:mzid mzML:mzid 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 mgf:pepXML mzML:mzid mzML:pepXML mzXML:mzid mzXML:pepXML |
| Comet (v2018.01 rev. 2) | mgf:pepXML mzML:pepXML mzXML:pepXML |
| Crux/Tide (v3.2) | mgf:pepXML mgf:mzid mzML:pepXML mzML:mzid mzXML:pepXML mzXML:mzid |
| MS Amanda (v2.0.0.11219) | mgf:csv(MS Amanda format) mzML:csv(MS Amanda format) |
| MSFragger (v20180316) | mzML:pepXML mzXML:pepXML |
| MaxQuant | version 1.3.0.5 version 1.5.3.30 version 1.5.4.1 version 1.5.7.4 version 1.5.8.3 version 1.6.2.3 version 1.6.5.0 |
| IPeak | mgf:mzid |
| IdentiPy (v0.2) | mgf:pepXML mzML:pepXML |
| MetaMorpheus (v0.0.286) | mzML:mzid |
| OMSSA (v2.1.9) | mgf:pepXML |
| Mascot (v2.5.1) | mgf:pepXML mgf:mzid mzML:pepXML mzML:mzid dat |
| Proteome Discoverer | TODO |
| ProteinPilot | TODO |
| PEAKS | TODO |
| pFind (>=v3.1.5) | Only supported MGF file search result |
| TPP (v5.1.0) | mzML:pepXML (Comet + PeptideProphet + iProphet + PTMProphet) |
| Software | Example files |
|---|---|
| Novor | mgf:csv (only support the Novor result generated through DeNovoGUI) |
| DeepNovo | mgf:txt |
| PepNovo+ | mgf:txt |
| pNovo+ | mgf:txt |
| Type | Example files |
|---|---|
| proBAM | ProBAM.tar.gz |
| proBed | ProBed.tar.gz |
Spectrum Library Central at PeptideAtlas
| Type | Example files |
|---|---|
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz |
| mzXML | SF_200217_U2OS_TiO2_HCD_OT_rep1.mzXML.gz |
PRIDE_Exp_Complete_Ac_22028.xml.gz
Please find an example in this tutorial: QC analysis.
PDV provides a command line module to produce figures of annotated spectra or TIC in batch mode. It can be used to generate figures according to a list of peptide sequences or a list of spectrum indexes.
$ java -jar PDV-1.1.0/PDV-1.1.0.jar -husage: Options
-a <arg> Error window for MS/MS fragment ion mass values. Unit is Da.
The default value is 0.5.
-ah Whether or not to consider neutral loss of H2O.
-an Whether or not to consider neutral loss of NH3.
-c <arg> The intensity percentile to consider for annotation. Default
is 3 (3%), it means that the peaks with intensities >= (3% *
max intensity) will be annotated.
-fh <arg> Figure height. Default is 400
-ft <arg> Figure type. Can be png, pdf or tiff.
-fu <arg> The units in which ‘height’(fh) and ‘width’(fw) are given.
Can be cm, mm or px. Default is px
-fw <arg> Figure width. Default is 800
-h Help
-help Help
-i <arg> A file containing peptide sequences or spectrum IDs. PDV will
generate figures for these peptides or spectra.
-k <arg> The input data type for parameter -i (Spectrum ID: s, peptide
sequence: p).
-o <arg> Output directory.
-pw <arg> Peak width. Default is 1
-r <arg> Identification file.
-rt <arg> Identification file format (mzIdentML: 1, pepXML: 2, proBAM:
3, txt: 4, maxQuant: 5, TIC: 6).
-s <arg> MS/MS data file
-st <arg> MS/MS data format (mgf: 1, mzML: 2, mzXML: 3).
Please find a few examples below. Please download the example data here: input_data.tar.gz
(1) Input: mgf and mzID
java -jar PDV-1.1.0/PDV-1.1.0.jar -r input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1_myrimatch_mgf.mzid -rt 1 -s input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf -st 1 -i input_data/spectrum_title.txt -k s -o output -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf(2) Input: mzML and mzID
java -jar PDV-1.1.0/PDV-1.1.0.jar -r input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1_myrimatch_mzML.mzid -rt 1 -s input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML -st 2 -i input_data/spectrum_scan_number.txt -k s -o output -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
(3) Input: mgf and pepXML
java -jar PDV-1.1.0/PDV-1.1.0.jar -r input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1_myrimatch_mgf.pepXML -rt 2 -s input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf -st 1 -i input_data/spectrum_title.txt -k s -o output -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
(4) Input mzML and pepXML
java -jar PDV-1.1.0/PDV-1.1.0.jar -r input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1_myrimatch_mzML.pepXML -rt 2 -s input_data/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML -st 2 -i input_data/spectrum_scan_number.txt -k s -o output -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
To cite the PDV package in publications, please use:
Li, K., et al. "PDV: an integrative proteomics data viewer." Bioinformatics, Volume 35, Issue 7, 01 April 2019, Pages 1249–1251. https://doi.org/10.1093/bioinformatics/bty770
PDV has been cited or used in the following manuscripts:
- Wang X, Codreanu S G, Wen B, et al. Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity. Molecular & Cellular Proteomics, 2017: mcp. RA117. 000155.
- Menschaert G, Wang X, Jones A R, et al. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome biology, 2018, 19(1): 12.
- Wen, Bo, Xiaojing Wang, and Bing Zhang. "PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations." Genome research 29.3 (2019): 485-493.
- Rong, Mingqiang, et al. "PPIP: Automated Software for Identification of Bioactive Endogenous Peptides." Journal of proteome research 18.2 (2018): 721-727.
- Zhang X, Huang H, He Y, et al. High-throughput identification of heavy metal binding proteins from the byssus of chinese green mussel (Perna viridis) by combination of transcriptome and proteome sequencing. PloS one, 2019, 14(5): e0216605.
- Ren, Zhe, et al. "Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets." Molecular & Cellular Proteomics 18.1 (2019): 86-98.
Contributions to the package are more than welcome.