#Peptideshaker download software#

We assist in the planning of your study, in the choice of appropriate analysis methods and/or the interpretation and presentation of obtained results. We provide consulting regarding statistics for proteomics and the statistical analysis of proteomics data as cooperation or service. Statistical consulting and analysis of proteomics data We provide consulting regarding bioinformatics for proteomics and the computational analysis of proteomics data as cooperation or service.

Curation of data sets uploaded to PRIDE from the DACH region (Germany, Austria, Switzerland)īioinformatics consulting and analysis of proteomics data.

Consulting concerning data provision and journal guidelines.

We offer support and consultancy services in the areas of Proteomics XML-based data standards and ontologies: This includes the creation and provision of a multi-level control system and the creation of quality controlled targeted proteomics databases.ĭata Standardization and conversion service We provide quality standards for proteomics experiments. Proteomics analysis suite for quality control, identification and quantification Next-generation visualization of protein consensus sequences. PAA adresses expert data analysts and developers. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation. Thereto, either a frequency-based backwards elimination approach or ensemble feature selection can be used. Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. After pre-processing (background correction, batch filtering, normalization) univariate feature pre-selection is performed (e.g., using the 'minimum M statistic' approach). gpr file format and can be extended easily to further data formats and technologies. It imports single color (protein) microarray data that has been saved in. ProtoArray data) for biomarker discovery. Protein Array Analyzer (PAA) is an R/Bioconductor package for protein microarray data analysis (esp.

#Peptideshaker download software#

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. In the present version, CrossPlatformCommander enables Integration data obtained from Proteomics and Transcriptomics measurements.

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 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. ProLiC includes different possibilities to solve the problem of protein list comparison: Spectral counting data from Excel into mzQuantML 1.0.ProteinScape 2.1 results into mzIdentML 1.1.Sequest.out or Comet.out files into mzIdentML 1.1.ProCon is a Java application for conversion of data from proteomics files or a LIMS into standard formats. ProCON - PROteomics CONversion tool (tool) 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. concluding the proteins from a set of identified spectra. The main focus of PIA lies on the integrated inference algorithms, i.e.

PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. PIA is a toolbox for MS based protein inference and identification analysis. PIA - Protein Inference Algorithms (tool)