BioInfra.Prot Services

PIA

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 lays 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. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

ProCon

ProCon is a Java 7 application for conversion of data from proteomics result files or a LIMS (Laboratory Information management System) database into the standard formats mzIdentML / PRIDE XML. In detail ProCon allows the conversion of: • peptide information of Sequest .out or Comet .out files into mzIdentML 1.1 • ProteomeDiscoverer 1.x (x=1, …, 4) .msf (and .prot.xml for PD 1.1 and PD 1.2) files into mzIdentML 1.1 • ProteinScape 1.3 results into PRIDE XML • ProteinScape 2.1 results into mzIdentML 1.1. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

Protein List Comparator

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. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

CrossPlatformCommander

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. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

PAA

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. Therefore, either a frequency-based backwards elimination aproach 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 is addressed to expert data analysts and developers. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

IceLogo

Next-generation visualization of protein consensus sequences. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

PeptideShaker

Proteomics analysis suite for quality control, identification and quantification
Funding: Service provision and maintenance funded by de.NBI.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

Quality standards

We provide quality standards for for proteomics experiments. This includes the creation and provision of a multi-level control system and the creation of quality controled targeted proteomics databases.
Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

Data standardisation and conversion service

The data standardisation and conversion service offers the following services for the users: • Consulting about ontologies, data standard formats, converters and upload tools in proteomics • Data conversion service • Data upload service via ProteomeXchange
Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

Bioinformatical consulting and analysis of proteomics data

We provide consulting regarding bioinformatics for proteomics and the computational analysis of proteomics data as cooperation or service.
Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

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.
Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

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.
Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

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
- MaxQuant
- 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

The toolbox can be used on our high-performance hardware infrastructure via high-bandwidth internet connection or at your site (via virtualization). Find this service in BioTools here.

Funding: Service provision and maintenance funded by de.NBI.

This email address is being protected from spambots. You need JavaScript enabled to view it.

LipidCreator

Computing precursor and fragment masses / formulas for lipids for targeted lipidomics

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

LipidXplorer

Identification and quantification of lipids within MS measurements for shotgun lipidomics

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

LUX Score

Tool for thecomprehensive comparison of lipidomes of different origins

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.