PIQMIe is a web-based tool for reliable analysis and visualization of semi-quantitative mass spectrometry (MS)-based proteomics data (Kuzniar and Kanaar, 2014). PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations, as obtained by the MaxQuant/Andromeda software (Cox et al., 2008, 2011), with additional biological information from the UniProtKB database, and makes the linked data available in the form of a light-weight relational database (SQLite). Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. PIQMIe provides data access via a web interface and programmatic RESTful API.
Python modules:
- cherrypy (>=3.2.2)
- genshi (>=0.7)
- sqlite3 (>=2.6.0)
- cairosvg (>=1.0.6)
- magic (>=0.4.3)
Javascript libraries:
- jQuery (>=1.11.0)
- jqGrid (>=4.6.0)
- D3.js (>=3.3.6)
git clone https://github.com/arnikz/PIQMIe.git
cd PIQMIe
virtualenv .venv
source .venv/bin/activate
pip install -r requirements.txt
Extract sample data on human bone development and mineralization (Alves et al., 2013).
cd data
tar xvf sampledata.tar.bz2
Edit config.ini
file depending on dev or prod mode.
#environment = "production"
server.socket_host = "127.0.0.1" # in prod: 0.0.0.0
server.socket_port = 8080 # in prod: 80
...
tools.staticdir.root = "<APP_BASE_DIR>"
tools.staticdir.dir = "PIQMIe"
tools.sessions.storage_path = "<DATA_DIR>" # default: PIQMIe/data
...
log.error_file = "error.log" # in prod: /var/log/piqmie/error.log
log.access_file = "access.log" # in prod: /var/log/piqmie/access.log
Start up the web server.
cd <APP_BASE_DIR>
cherryd -i PIQMIe -c PIQMIe/config.ini # in prod: sudo ...
To view the sample data on your local PIQMIe instance, follow Sample Data tab and click on results.
Alternatively, upload your own data files, i.e., MaxQuant peptide (evidence.txt
) and protein (proteinGroups.txt
) lists including the sequence library in FASTA (.fa|fasta
), to the web server and click on the Submit button to process the input files. After processing, click on the generated link to view the results. Note: For each session, a new (sub)directory <DATA_DIR>/<jobID>
including I/O files will be created.
Kuzniar, A. and Kanaar, R. (2014) PIQMIe: a web server for semi-quantitative proteomics data management and analysis, Nucleic Acids Research, 42, W100–W106. doi:10.1093/nar/gku478
Kuzniar, A. PIQMIe version 1.0. doi:10.5281/zenodo.34090