PDV: an integrative proteomics data viewer
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README.md

PDV: an integrative proteomics data viewer

Join the chat at https://gitter.im/PDV-public/Lobby Downloads Release

PDV is a JAVA tool for proteomics data visualization.

Usage

A user's manual is available at http://pdv.zhang-lab.org.

Installation

The PDV package can be downloaded at https://github.com/wenbostar/PDV/releases.

Example

Database searching:

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 1.5.5.1
version 1.5.8.3
version 1.6.0.1
version 1.6.2.3
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
TPP (v5.1.0) mzML:pepXML (Comet + PeptideProphet + iProphet + PTMProphet)

Denovo sequencing:

Software Example files
Novor mgf:csv (only support the Novor result generated through DeNovoGUI)
DeepNovo mgf:txt
PepNovo+ mgf:txt
pNovo+ mgf:txt

Proteogenomics:

Type Example files
proBAM ProBAM.tar.gz
proBed ProBed.tar.gz

One PSM:

Spectrum library:

Spectrum Library Central at PeptideAtlas

MS data:

Type Example files
mzML SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz
mzXML SF_200217_U2OS_TiO2_HCD_OT_rep1.mzXML.gz

PRIDE XML:

PRIDE_Exp_Complete_Ac_22028.xml.gz

QC analysis:

Please find an example in this tutorial: QC analysis.

Command line:

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 -h
usage: 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

Citation

To cite the PDV package in publications, please use:

Li, K., et al. (2018). "PDV: an integrative proteomics data viewer." Bioinformatics, 2018. doi: 10.1093/bioinformatics/bty770

List of citations

PDV has been cited in the following manuscripts:

  1. 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.
  2. 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.

Contribution

Contributions to the package are more than welcome.

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