Proteome Discoverer™ includes the following:
- NEW! – Improved Tandem Mass Tags™ (TMT) quantitation including statistical analysis of the results
- NEW! – Flexible handling of peptide identification for improved coverage and relative quantitation
- NEW! – Proteome Discoverer Daemon works with Thermo Scientific Xcalibur instrument control software to allow automated data processing following data collection
- Industry-standard database search algorithms SEQUEST and Mascot (optional) for confident and comprehensive protein identification and PTM characterization
- Z-Core database search algorithm for quick and easy searching of ETD data
- Ability to easily combine results of multiple search engines and dissociation techniques (CID, HCD, ETD) in a single consensus report
- False Discovery Rate (FDR) for each search for validation of protein IDs
- Simple wizards and customizable workflows to analyze MSn data from raw spectra through protein annotation
- Support for data standards developed by the HUPO Proteomics Standards Initiative (PSI)
- Annotation capability to add biological information about proteins identified
- Exclusion list generation for Xcalibur™ software, allowing intelligent iterative interrogation of samples
- SRF file import wizard for seamless transition from older Thermo Scientific BioWorks software
Proteome Discoverer software accommodates several relative quantitation methods, including common isobaric mass tagging techniques such as TMT technology, reporting the peptides identified and their relative expression ratios in a simple graphical display and now includes autaomated statistical analysis of the results. Customizable filters can be designed to use only unique peptides to calculate accurate relative protein quantitation, and allows manual removal of individual results. Normalization of peptide concentration corrects for experimental errors.
The software provides full multiconsensus analysis capabilities to allow results from two or more raw files to be combined into a single results file. Multiple results files can be combined into a single display file as either a combined set of replicates or as separate studies for comparative purposes. Multiple large results files can be rapidly loaded using the pre-filtering function to remove low-confidence results prior to display.
Proteome Discoverer Daemon works with Xcalibur software™ to allow automated data processing following data collection.
Proteome Discoverer software contains several database search engines to complement the breadth of dissociation techniques such as CID, ETD, and HCD available with Thermo Scientific LTQ series linear ion trap mass spectrometers. Different dissociation techniques provide complementary results and often increase protein coverage and the number of identified proteins, allowing users to exploit the benefits of their high-mass-accuracy, high-resolution data.
The Peptide Consensus View facilitates interpretation of database search results by combining CID and ETD fragment ion matches to increase peptide coverage. Multiple complex data sets are easily organized and advanced visualization tools facilitate data interpretation and results sharing.
The Proteome Discoverer Workflow Editor allows the user to select from a comprehensive menu of search algorithms, dissociation methods, results filters and quantitative methods to set up a custom workflow, and even consolidate the results in a single easy-to-read report. In addition, the PMF Workflow facilitates analysis of high-mass-accuracy MALDI data.
The novel database search algorithm, Z-Core, specifically takes into account the unique characteristics of ETD spectra. It includes a data pre-processing step that assigns a charge state to precursor ions from unit resolution measurements according to the characteristics of ETD spectra, such as intense charge-reduced precursor ion peaks. Z-Core increases the throughput of ETD data analysis, maximizes database search efficiency, increases the confidence of the subsequent identification results and reduces the time necessary for ETD data interrogation.
Proteome Discoverer software provides annotation workflows for LC-MS/MS data through the InforSense Platform that automatically retrieves pertinent information about each identified protein from public databases, providing annotation including GO (Gene Ontology) classifications, sites of posttranslational modifications (PTMs), and literature references. Annotation capabilities such as these provide specific biological information about proteins and their post-translational modifications and can be used to help design iterative and targeted follow-up experiments. Additionally, identification results annotated with Meta information from public databases are easily exported to Microsoft Excel and the data can be further interrogated to verify known and predicted post-translational modifications and view other descriptive information for each.
LC-MSn data acquisition can now be combined with creative data interrogation strategies via creation of inclusion and exclusion lists for direct import into Xcalibur instrument methods, and iterative workflows can be created to specifically look for low-level sample components.
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