BioInfra.Prot services at a glance

Most of our software tools and some other open proteomics tools are also available in the pre-installed and pre-configured Proteomics Toolbox provided by the de.NBI-service center BioInfra.Prot.
The toolbox can be used on our hardware infrastructure via a high-bandwidth internet connection and has the advantage that you benefit from our high-performance multi-kernel computing environment providing enough main memory and storage space.

If you want to use this Proteomics Toolbox or have further questions, please contact us at

Service Description Link/Contact
PIA - Protein Inference Algorithms (tool) PIA is a toolbox for MS based protein inference and identification analysis.

PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lies on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins.
download & info:

ProCON - PROteomics CONversion tool (tool) ProCon is a Java application for conversion of data from proteomics files or a LIMS into standard formats. It allows the conversion of

· Sequest.out or Comet.out files into mzIdentML 1.1

· ProteomeDiscoverer 1.1 – 1.4 .msf file information into mzIdentML 1.1

· ProteinScape 1.3 results into PRIDE XML

· ProteinScape 2.1 results into mzIdentML 1.1

· Spectral counting data from Excel into mzQuantML 1.0
download & info:

ProLiC - PROtein LIst Comparator (tool) ProLiC includes different possibilities to solve the problem of protein list comparison:
In addition to a simple accession based comparison, which is still supported by the software, ProLiC permits a more reliable comparison of protein lists from different protein databases by considering measured sequence and/or peptide information.
download & info:

XPlatCom – Cross PLATform COMmander
Our CrossPlatformCommander tool facilitates several steps that frequently occur in the context of multi-OMICS workflows like data conversion, quality control, data comparison, text mining and statistical analyses in a semi-automatic manner. In the present version, CrossPlatformCommander enables Integration data obtained from Proteomics and Transcriptomics measurements. However, the software is currently under extensive reconstruction and adaption (Implementation as a node in the KNIME workflow engine, integration of data obtained from additional OMICS platforms, support of additional data formats etc.) in order to meet the needs of de.NBI. download & info:

PAA – Protein Array Analyzer (tool) Protein Array Analyzer (PAA) is an R/Bioconductor package for protein microarray data analysis (esp. ProtoArray data) for biomarker discovery. It imports single color (protein) microarray data that has been saved in .gpr file format and can be extended easily to further data formats and technologies. After pre-processing (background correction, batch filtering, normalization) univariate feature pre-selection is performed (e.g., using the "minimum M statistic" approach). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Thereto, either a frequency-based backwards elimination approach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation. PAA adresses expert data analysts and developers. download & info:

IceLogo (tool) Next-generation visualization of protein consensus sequences. download & info:

PeptideShaker (tool) Proteomics analysis suite for quality control, identification and quantification download & info:

Quality Standards We provide quality standards for proteomics experiments. This includes the creation and provision of a multi-level control system and the creation of quality controlled targeted proteomics databases.
Data Standardization and conversion service We offer support and consultancy services in the areas of Proteomics XML-based data standards and ontologies:

· Consulting concerning data provision and journal guidelines

· Data conversion service

· Data upload service via ProteomeXchange

· CV maintenance as a community service

· Provision of converters, e.g. ProCon

· Curation of data sets uploaded to PRIDE from the DACH region (Germany, Austria, Switzerland)
Bioinformatics consulting and analysis of proteomics data We provide consulting regarding bioinformatics for proteomics and the computational analysis of proteomics data as cooperation or service.
Statistical consulting and analysis of proteomics data We provide consulting regarding statistics for proteomics and the statistical analysis of proteomics data as cooperation or service.

We assist in the planning of your study, in the choice of appropriate analysis methods and/or the interpretation and presentation of obtained results. Beyond the expert advice given by our educated biometricians, we also offer to conduct the respective analyses as agreed.
Hardware Sharing We share our large high-performance hardware resources (i.e., storage and compute cluster) via high bandwidth internet connection (DFN link) for a limited period of time as service.
Proteomics Toolbox We provide a proteomics software toolbox (i.e., offering pre-installed, pre-configured and tested own tools and free third-party software) on our hardware infrastructure.

The current version of the Proteomics Toolbox contains the
following software tools:

- Protein Inference Algorithms (PIA)
- ProtoArray Analyzer (PAA)
- Protein List Comparison (ProLiC)
- PeptideShaker, SearchGUI
- for MRM / AQUA calibration: CalibraCurve
- MS tool suite: OpenMS
- Targeted Proteomics Environment: Skyline
- workflow environment: KNIME Analytics Platform
- spectrum identification search engines: X!TAndem, OMSSA, MS-GF+, Myrimatch (via KNIME nodes, but also executable as standalone)
- conversion tools ProCon, ProteoWizard
- selected frequently used protein databases
- statistics environment: R & R Studio
- MaxQuant

The toolbox can be used on our high-performance hardware
infrastructure via high-bandwidth internet connection
or at your site (via virtualization)


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Central BioInfra.Prot contact:

Link to BioInfra.Prot project partner (Leibniz Institute ISAS, Dortmund):


(FKZ 031 A 534A & B)