OmicsHub™ Proteomics

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract OmicsHub Proteomics is an integrated proteomics solution allowing protein peak detection or filtering, to protein identification, annotation and final reports.

It has been designed as a central data management system that allows the user to collect, annotate and conduct qualitative and quantitative analysis of Mass Spectrometry (MS) data.

Users can automate tasks; however, OmicsHub Proteomics remains flexible enough to allow manual control of final validation.

OmicsHub Proteomics supports both Liquid Chromatography (LC) and 2D-gel workflows and can be easily extended to meet custom laboratory needs with minimal effort.

Its configuration allows users to process experiments in both parallel and concurrent modes simultaneously through customized pipelines (workflows).

Identified proteins obtained as a result of Peptide Mass Fingerprint (PMF) and/or Peptide Fragmentation Fingerprint (PFF) in commonly used search engines is processed by OmicsHub Proteomics to automatically remove any redundancies.

It provides a quick and clear estimate of how many different protein families have been obtained.

Furthermore, biological information extracted from a dynamic list of sources, including pathways information, can be used to annotate resulting proteins. This enables better understanding of the protein’s role according to a specific experiment and/or project.

Proteomics data can be exported in the PRIDE format enabling lab users to easily share and publish their experimental results. When providing services externally, custom HTML reports including descriptive images can also be generated by OmicsHub Proteomics.

The manufacturer believes that one of the most time consuming tasks in a proteomics laboratory facility is generating customized reports, however with OmicsHub Proteomics generating customized report(s) takes just a click!

Benefits of OmicsHub Proteomics -

This end to end server solution fits into any proteomics bioinformatics lab infrastructure. It has a web-based interface for multi-user access needing only a web browser to start using it.

Specific attention has been placed on its usability, to make it easy to use and intuitive, including the option to run semi-automatic workflows for batch protein searching, quantification and statistical analysis, reducing human error, time and data management complexity.

Most of the methods implemented are general and follow published standards. They were designed in collaboration with experienced proteomics groups from the Spanish National Institute of Proteomics.

OmicsHub Proteomics Project Lifecycle --

1) Experiment annotation with standards - The OmicsHub experiment database scheme has been designed to follow the FuGE (Functional Genomics Experiment) and PRIDE (PRoteomics IDEntifications) standards.

The system includes Ontology databases for controlled vocabulary including the Proteomics Standards Initiative (PSI)-MS.

2) Import of instrument data - OmicsHub Proteomics has been designed to be widely compatible with mass spectrometer instruments.

This enables OmicsHub Proteomics to be compatible with any mass spectrometer irrespective of make or brand and to integrate all the data in your lab. OmicsHub Proteomics guides the user during every step of the instrument data acquisition process.

3) Protein batch searches - OmicsHub Proteomics allows batch Protein Peptide identification with full false discovery rate (FDR) control search engines [e.g. Mascot - (see G6G Abstract Number 20087) and Phenyx - (see G6G Abstract Number 20080)].

The search engines can be accessed from within the OmicsHub Proteomics platform and the results can be viewed and compared in the same pane.

Updates will include software intelligence to choose the most appropriate search result for a given experiment.

4) Analysis of results - OmicsHub Proteomics provides advanced analysis and interpretation of data.

Once the proteins are identified OmicsHub provides the ability to group these proteins into families, removing redundancy. Peak filtering and protein filtering is also possible.

An added feature of OmicsHub Proteomics is that OmicsHub users can automatically retrieve protein functional annotation.

Pathway(s) integration with Ingenuity IPA - (see G6G Abstract Number 20017U) is implemented from within the OmicsHub Proteomics platform.

5) Reporting - OmicsHub Proteomics provides advanced and flexible reporting capabilities. The final reports can be generated in the HTML and PRIDE format thereby making it easier for the user to adhere to standards.

Reports are customizable and can include the entire experiment data or specific outputs as desired by the user.

OmicsHub™ Proteomics Version 2.0 features include:

1) Protein Quantification;

2) Pathway Viewer Integrated;

3) Improved automatic Reports (PRIDE and HTML);

4) Protein Validation;

5) Background importation;

6) User roles and permissions;

7) Protein functional annotation (UniProt, InterPro, GO, Panther, etc.);

8) Guided workflow;

9) Multi-user all-in-one web-based platform;

10) Controlled vocabulary for experiment annotation;

11) Protein experiments database;

12) Integration of multiple MS instruments;

13) Batch searches on Mascot, Phenyx and OMSSA;

14) Supports collaborative/multi-centric projects or client access; and

15) FDA 21 CFR part 11 recommendations, partially compliant.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site OmicsHub Proteomics

Price Contact manufacturer.

G6G Abstract Number 20664

G6G Manufacturer Number 101520