Robust and flexible scoring: the Phenyx scoring algorithm (based on OLAV) is published and designed to meet the demands of high-throughput MS data analysis
Phenyx/OLAV was validated in an industrial high-throughput environment running on 1,400 processors.
Our scoring schemes have been tailored for a number of instruments supplied by major MS instrument providers, such as Applied Biosystems, Bruker Daltonics, Shimadzu, Thermo Electron, and Waters-Micromass, thus ensuring high results accuracy while using a wide variety of currently available hardware.
Thanks to their flexibility, Phenyx scoring schemes can, in addition, be optimized for your own instrumentation and workflow in order to best fit your specific MS environment, enabling you to add pertinence to and to take great benefit from your mass spectrometry data.
For more detailed information, please see Understanding Phenyx: The Scoring System
Flexible and interactive interface: the Phenyx Web Interface enables you to fine-tune your data submission and to seamlessly assess and validate your results using a range of dynamic views, reports and graphics
Submission window: Two-round search, submission parameters
Phenyx performs searches in one or two serial steps called rounds.
A classical one-round search is performed on a defined set of proteins (i.e. when a full database or taxonomy or accession number (AC) is selected). Identified peptides that fulfil the z-Score and p-Value thresholds are accepted and the corresponding protein is validated.
The basic principle of two rounds is that the first round processes all the proteins in the designated search space and the second round only processes the proteins that passed the first round. The first round parameters need to be stringent enough to sufficiently validate protein identification (i.e. a few good peptides). The second round parameters enable you to open the search criteria in order to increase the sequence coverage, by searching for combinatorial modifications or other special features. A two-round search therefore identifies proteins according to a first set of parameters and then performs a more exhaustive search on the proteins while saving computation time and reducing the random match rate.
For detailed information about the available submission parameters on Phenyx, please see Understanding Phenyx: The Effect of Submission Parameters on Result Accuracy
Seamlessly assess and validate your results with a full range of graphic and dynamic views
Proteins Overview (protein centric view): A summary of the identification results (list of proteins and peptides). The Proteins Overview is divided into three panes: Best-scoring Protein Table (top left), Protein Details (top right) and Peptide Match Table (bottom).
Compounds Overview (spectrum centric view): All mass spectra that were matched during the search are listed with their corresponding peptide identifications and protein affiliations.
Peptide Match Details: A peptide match is the pairing of an experimental fragmentation spectrum to a theoretical segment of a protein. This dynamic view represents the peptide match with its spectrum interpretation and with a colored table describing the set identified fragment ions.
Protein Match Details: For a given protein, this dynamic view shows the list of identified peptides followed by two different graphical representations of the protein sequence and its coverage.
Extensive use of annotations in databases, notably in Swiss-Prot (PTMs, variants, AA modifications...)
If a highly annotated database such as UniProt_Swiss-Prot is utilized, many of the annotations are considered during the search. For example, Phenyx processes the entries and generates separate entities for each splicing variant or searches for post-translationally modified amino acids if the corresponding annotations exist.
Enhanced accuracy and reliability of your MS data identification through the unique Conflict Resolution algorithm and Manual Validation functionality
A conflict can occur during scoring when a mass spectrum matches more than one peptide sequence in the selected databases. A given spectrum should ideally correlate to a unique molecular structure, except if a spectrum represents a mixture of peptides. When more than one peptide reasonably matches a MS/MS spectrum, should the scoring algorithm deal with them?
- Yes: Phenyx can distinguish all possible matches and decide which is/are the most probable.
- No: Phenyx simply reports all sequences matching with an acceptable score. Then when the results are available, you deal personally with any questionable spectra having multiple matches.
Users can manually validate/invalidate Phenyx results; this means that the validation status of peptide matches can be accepted or rejected. The modification can be stored to keep track of the manual changes. The effect of the manual validation, available in the Compounds Overview as checkboxes, is reported in all other views, such as the Proteins Overview, the Protein Match Details view, the Excel export, etc.
Compare and assess results in one shot with the Results Comparison functionality
Compare your Phenyx runs amongst themselves and with those of other MS search engines like Mascot, SEQUEST, X!Tandem and Popitam
Visualize in various levels of granularity, including protein groups, proteins, peptides, and interpreted spectra
Align proteins from searches in different databanks
One-click export for quick publication
Batch submission via the Phenyx Daemon
The Phenyx Daemon is designed to perform automated submissions of MS/MS spectra to Phenyx. A batch experiment in the Phenyx Daemon submits mass spectra to a workflow. This workflow is a set of dependant actions that can run on a local system or on a remote server. Typically, these actions can include pre-processing steps such as data filtering and format conversion as well as submission to Phenyx as search engine. The Daemon keeps track of already submitted datasets and displays the status of jobs in a session.
View the Phenyx Daemon Tutorial Movie.
(minimum 768MB RAM required)
Easy integration with your Proteomics pipeline
Phenyx uses XML and text files extensively to store and define data, parameters, configuration, etc. Communication and manipulation of these resources is primarily made using Perl modules.
Phenyx provides secured Web services to remotely submit peak lists to the engine, monitor search progress, and retrieve results files.
Pre and post processing can be configured to enhance the identification process and then facilitate its integration in third party tools (and your own bioinformatics tools/pipeline). Expressionist (GeneData), TPP (Institute for Systems Biology), IPP (Insilicos), ProteinScape (Bruker Daltonics), Proteus (GenoLogics), Scaffold (Proteome Software), Sorcerer (Sage-N Research) are just a few examples of solutions and tools integrating Phenyx. See also the Export Jobs section below for more details.
Export jobs for reporting or further processing
This functionality allows to post-process one or more jobs and create reports to be used as is or to be integrated in a post-analysis automated pipeline. These include, non exhaustively: a publication-compatible excel report file (MCP export), a False Discovery Rate (FDR) full report to fine tune the confidence level in the results, an error distribution report to QC the calibration status of your MS instrumentation, etc.
A number of these reports are available to integrate third party tools, such as Scaffold, TPP, Progenesis LC-MS, MSight.
Access all details of one or more given job(s) and export it(them) in an archive.
Customized reports: additional exports can be generated that incorporate external parsers, statistics and other post-processing software. Include Phenyx in your data processing and data management system.
Configurable Management Console
The Management Console is the place to perform a number of tasks associated with identification and quantitation. This include a number of system and user configuration actions, the use of import, export and maintenance functionalities, within others. Some of these are available to all users, some are more restricted. The console allows users to work in a personalized environment:
Define your own AA modifications and cleavage rules to best accommodate with your experimental conditions.
Upload private databanks to quickly match peptides with your own sequences.
Import results from other Phenyx users and servers or search engines like Mascot, SEQUEST, X!Tandem and Popitam to visualize, compare and validate these jobs within the Phenyx Web interface.
Access a number of predefined and customizable set of reports. See the Export Jobs section for more details.
Access additional tools to perform peak list format conversion and filtering.
Admin users have additional access to a number of server configuration and monitoring options such as management of users, control and statistics on the server activities, configuration of the steps of a Phenyx run, etc.
Enhanced server functionalities
Jobs are properties of a user. A user can decide to share access to selected jobs. Access rights means: a job result can be visualized, altered via manual validation and resubmitted or deleted by another user; in a typical service lab, a user can run a job, another can validate it, and the customer can only visualize and export the result.
Additional properties and features can be attributed to users, such as: access to specific scoring models, submission profiles, dedicated reports, taxonomy trees, search space limits, submission limits, priorities on jobs, etc.
Phenyx has implemented a powerful and flexible queuing system to manage users and jobs priorities. You can decide which user has priority over others to access the calculation resource; you can also attribute a maximum number of simultaneous calculation nodes per user queue.
New in 2.6: Extended PTM search
Phenyx integrates an in-house algorithm to look for a large number of amino acid modifications. The extended PTM search can be activated in the 2-round, and enables you to considerably increase your sequence coverage. In addition to default and user-defined AA modifications, Phenyx also embeds an "Extended PTM database" that prepares a much larger list of AA modifications to be queried to help in PTM discovery. GeneBio also distributes Modiro
®, Protagen's PTM discovery software, to complement its MS analysis suite.
Modiro is a fast and automated solution to extensively detect true post-translational modifications in MS/MS datasets. Phenyx provides a specific export to be searched with Modiro and both software platforms will soon be seamlessly interfaced to automate PTM discovery.
For more detailed information, please see Extended PTM Search
New in 2.6: Cross-linked peptides identification
Phenyx helps the structural characterization of protein interactions, for instance of protein complexes, via the use of cross-linkers.
One promising approach is to add chemical cross-linkers to protein complexes and to identify cross-linked peptides. This allows for the identification of partner proteins in a complex, and for the determination of the contact positions between interacting proteins.
Just select the protein(s) of interest and describe the chemical and reactivity properties of a chosen cross-linker. Phenyx will prepare a dedicated database and perform a search from your MS data. Candidate cross-lined peptides are easily recognized in various views.
What the feature brings you:
- Takes advantage of high-mass accuracy to identify cross-linked peptides with high confidence
- Drastically reduces interpretation time
- A detailed visualization of cross-linked peptides (and their respective binding sites) in specific dynamics views
- No limitations to the definition of cross-linkers (size, amino acid specificity)
- Works for inter and intra-molecular cross-linking events
- Allows for analysis on multiple protein complexes (up to 50 different protein sequences in a complex)
For more details , please see the presentation
here.
New in 2.6: Quantitation module for simple to highly complex workflows
- Phenyx supports isobaric tags (iTRAQ, Tandem Mass Tag,...) and label-free quantitation via spectral counting
- Quantify simple to highly complex analyses workflows in one shot: multiple identification runs, replicates concept and multi-state analysis (time course experiments...)
- Powerful statistical strategy provides normalization test and outliers removal
- Global and detailed reports/graphical representations of the distribution of proteins and peptides ratios
For more detailed information, please see Phenyx Quantitation Module.
New in 2.6: Enhanced Databank Manager
Enhanced Databank Manager for quick and simple database installation and maintenance:
- Install and update any proprietary or public sequence databanks thanks to the graphical interface of the Databank Manager
- Maintain different versions of databanks
- Possibility to prepare a decoy version of any databank in one click
- Phenyx accepts proteomics and nucleotides databanks
- Databanks can be attributed to all users or restricted to one user
- Each user can create its own set of private databases, providing it has the right to do so.
For more detailed information, please see Phenyx DB Manager.
Using ProteinCenter, you can now confidently interpret large data sets to produce meaningful biological information within minutes. ProteinCenter makes data interpretation simpler, faster and more reliable, allowing you to:
