Proteome Discoverer

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract Thermo Scientific Proteome Discoverer software is a flexible, expandable platform for the analysis of qualitative and quantitative proteomics data.

Outstanding sensitivity and the rapid growth of public databases have made mass spectrometry (M/S) the primary method of identifying proteins in complex biological samples.

While database search algorithms such as SEQUEST - (see G6G Abstract Number 20285) and MASCOT - (see G6G Abstract Number 20087), have existed for over a decade to facilitate the identification of proteins from mass spectral data, the field of proteomics continues to expand and with it the need for more advanced and flexible software tools to interpret the data.

Proteome Discoverer was designed to address this need for flexibility by offering a wide array of bio-software tools and customizable workflows for every proteomics experiment.

Proteome Discoverer software is a comprehensive tool for proteomic data analysis.

It supports multiple dissociation techniques, quantitation technologies, and database search algorithms for more confident and comprehensive protein identification and characterization.

The Proteome Discoverer Daemon facilitates automated data analysis, for greater productivity.

Proteome Discoverer Key Features and Benefits --

1) Multiple database search capability provides the option of applying multiple search algorithms (SEQUEST, Z-Core, MASCOT, etc.) and combining their outputs to maximize and cross-validate results;

2) Support for multiple dissociation techniques (CID, ETD, and HCD) and the ability to combine their results helps identify more Post-Translational Modifications (PTMs) and increase confidence in those identifications;

3) Support for isobaric mass tagging (TMT, iTRAQ), and HeavyPeptide techniques enable relative or absolute quantitation;

4) A Mascot-based peptide mass fingerprinting workflow leverages high-mass-accuracy Matrix-Assisted Laser Desorption/Ionization (MALDI) data;

5) False Discovery Rate (FDR) determination validates protein IDs;

6) Wizards and customizable proteomics workflows simplify analysis of MSn data from raw spectra through protein annotation;

7) Automated annotation of identified proteins with Gene Ontology (GO) classifications, PTMs, and literature references from public databases illustrates biological context;

8) Creative data interrogation strategies such as generating inclusion and exclusion lists and import those lists directly into instrument methods enable more effective location of low-level sample components;

9) Support for data standards developed by the HUPO Proteomics Standards Initiative (PSI) facilitates data comparison, exchange, and verification;

10) SRF file import wizard provides a seamless transition from the Thermo Scientific BioWorks platform; and

11) Robust Proteome Discoverer software platform can be expanded through integration of custom software tools.

Proteome Discoverer is compatible with --

1) Xcalibur software - Thermo Scientific Xcalibur software is a flexible Windows-based data system that provides instrument control and data analysis for the entire family of Thermo Scientific mass spectrometers and related instruments.

2) SIEVE software - Thermo Scientific SIEVE software is an automated solution for the label-free, semi-quantitative differential expression analysis of proteins, peptides and metabolites.

3) ProSightPC software - Thermo Scientific ProSightPC is one of the first stand-alone software products for analyzing top-down proteomics data, and it has been enhanced to add support for middle-down and bottom-up experiments, making it an all-around tool for identification and characterization of both intact proteins and peptides.

ProSightPC 2.0 software enables high-throughput processing of all accurate-mass MS/MS data, whether from top-down, middle-down or bottom-up experiments including the characterization of proteins with known PTMs.

4) PEAKS Studio software - Thermo Scientific offers PEAKS Studio software for de novo sequencing produced by Bioinformatics Solutions of Waterloo, Canada - (see G6G Abstract Number 20085).

A fully functional proteomics workbench, PEAKS Studio will perform de novo sequencing, protein identification, meta-protein identification (PEAKS inChorus), assisted manual sequencing and data manipulation, either along side PEAKS Online or independently.

5) ProMass Deconvolution software - Thermo Scientific* ProMass Deconvolution 2.5 is an automated biomolecule deconvolution and reporting software package that produces artifact-free deconvoluted ESI mass spectra of biomolecules.

ProMass Deconvolution 2.5 software is ideal for the analysis of intact proteins and oligonucleotides and is optimized for high-throughput proteomics research.

6) LTQ family of linear ion trap mass spectrometers.

7) LTQ Obritrap family of hybrid mass spectrometers.

8) LTQ Ultra hybrid mass spectrometers.

9) Electron Transfer Dissociation (ETD) - Thermo Scientific Electron Transfer Dissociation (ETD) is an advanced fragmentation technique that complements traditional collision-induced dissociation (CID).

10) TSQ family of triple quadrupole mass spectrometers.

System Requirements

Contact manufacturer.


Manufacturer Web Site Proteome Discoverer

Price Contact manufacturer.

G6G Abstract Number 20284R

G6G Manufacturer Number 102650