Versions of PEAKS

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Past & Present PEAKS Versions

PEAKS Online

Improvements to de novo Sequencing

  • Interactive Protein Coverage View
  • New Automatic de novo Result Validation
  • Improved de novo Residue Local Confidence Score
  • CID/HCD/ETD Complementary Fragmentation Support

New Label Free Quantification Module

  • Enhanced Feature Detection – Expectation Maximum (EM) algorithm
  • Significant improvement to -10LgP Score for Peptide Features and Proteins
  • New RT Alignment Algorithm
  • Normalization using TIC or selected protein(s)

Projects, Processing & Review

  • Improved speed for PEAKS DB, PEAKS PTM and SPIDER
  • Much improved data 2D/3D heatmap visualization and navigation
  • New project wizard to facilitate the creation of complex project with a large number of samples and fractions
  • Reduced false discovery on PEAKS PTM algorithm

Collaborate

  • Better support for Thermo and Agilent raw files on 64bit OS
  • Pepxml exported from PEAKS can be imported into Skyline
  • Better support on mzidentML (version 1.1) format
  • Support pepxml exported from PD 1.4
  • Improved 3rd party exporting to Scaffold and resolved PTM issue
  • Fixed mzIdentML protein reporting issue
  • Fixed a regression bug affecting charge and mass correction on high charge Orbitrap data
  • Third party and pepXML export from inChorus results are now disabled. It was unintentionally opened in the initial PEAKS 7 release. In mzIdentML, there are currently no CV term in the standard for PEAKS inChorus results.
  • Unique peptide filter in Label Free Quantification results now correctly uses the unique peptides instead of the peptide features as the filter
  • Fixed an issue in Label Free Quantification p-value calculation. Users do not need to redo the analysis. Re-open the results will have the p-value displayed correctly
  • PEAKS now supports 64 bit CompassXtract libraries from Bruker
  • PEAKS now can read the scan number from MGF files generated by the new Compass tools
  • Better handling on MGF/PKL/DTA files with excessive white spaces
  • Better handling on importing Mascot results into PEAKS. Solved issues for some custom FASTA header formats
  • Resolved slowe Derby initialization issue.
  • PEAKS project converter: MS1 spectrum information is correctly converted from PEAKS 6 projects
  • Added Mascot 2.5 support in inChorus
  • Better support on Waters raw data
  • Fixed an issue related to usage when using a different user account
  • Fixed an issue in mzIdentML exporting when some fractions had no results
  • Fixed an issue reading Bruker raw data
  • Fixed an issue that caused OMSSA search to sometimes fail after a Mascot search

Algorithm

  • New nonspecific enzyme digestion support. Now one can allow nonspecific enzyme digestion at 0, 1, or both ends of a peptide. Having more nonspecific digestion ends will increase the search sensitivity at a reduced search speed.
  • Consider neutral loss of phosphorylation and sulfation PTMs in the scoring functions of PEAKS DB and PEAKS PTM
  • Newly support protein N-term PTMs
  • New -10lgP score and FDR control for PTM and SPIDER results
  • FDR control of the inChorus result. Different search engines results can now be combined according to a unified FDR for each search engine.
  • Improved precursor mass correction. The mass correction function in “data refine” step recognizes the real monoisotopic mass even if the instrument’s raw data reported the isotope mass. The algorithm is improved in the new version.

GUI Improvements

  • Easier PTM selection interface. The PTMs are separated in three “common”, “uncommon”, “customized” to make it easy to specify the PTMs to search for. Additionally, a “Recent” list includes all the PTMs recently used by the user.
  • De novo only view added to inChorus result. The de novo only view reports peptides found exclusively by de novo sequencing. This useful view is now available to the inChorus result too.
  • Improved spectrum annotation view. Mouse over an amino acid in the spectrum annotation will highlight the supporting fragment ions. Setting an anchor peak will show mass different between the current peak and the anchor peak.
  • Improved project creation interface. The selection of instrument type and fragmentation mode is easier. Users can specify a proteolysis enzyme for each sample at the project creation interface.
  • More searching functions to locate a specific de novo sequence result. Now de novo sequencing results can be sorted and searched with the amino acid sequence.
  • Display absolute intensity in PEAKS Q. Users now can choose to display absolute intensities or ratios in PEAKS Q results. For ratio display, users can choose which sample the ratio is based.
  • More statistics in the summary view. The PTM profile table is improved. A protein FDR value is added.
  • One-click specification of common FDR values (e.g. 1%) in the FDR selection pane.

Better Community Support

  • A new configuration wizard to assist the download and installation of public protein databases and raw file readers/converters.
  • Major accuracy and sensitivity improvement on the analysis of AB SCIEX TripleTOF data.
  • Proteome Discover support. Now PEAKS can load the pepXML result file generated from Thermo’s Proteome Discover software.
  • Support mzIdentML result format. Now PEAKS can export mzIdentML file for downstream analysis such as Scaffold PTM.
  • Export high resolution images of the spectrum annotation and protein coverage view.
  • Export to website or single webpage format for easy sharing of results.

Unprecedented accuracy and sensitivity for database search

  • The revamped database search engine (PEAKS DB) results in substantially improved accuracy and sensitivity for peptide identification, causing the identification of more peptides with a reduced false discovery rate (FDR). In particular, the preview version of the PEAKS DB engine produced excellent performance in the ABRF/iPRG 2011 study for ETD data analysis.

Comprehensive result visualization

  • Numerous improvements were made to support the visual examination of the results from all different angles. To enhance user confidence, PEAKS provides tools for vigorous yet convenient result examination.
  • Users will also notice many areas where a summary of the result’s statistics are automatically provided. Through these charts users can easily answer important questions such as whether the target-decoy FDR calculation is reliable, and whether the instrument is well-calibrated. Additionally, the peptide and protein tables were rewritten to provide convenient search and sorting functions, allowing easy location and examination of certain particularly interesting peptides or proteins.

Built-in result validation

  • PEAKS DB provides a seamlessly built-in result validation system with an enhanced target decoy method. Score thresholds can be conveniently selected from the FDR curve, avoiding the guess work performed with other software.

Enhanced result reporting

  • The new summary view provides a central place for specifying score thresholds to filter results. Results can be filtered quickly and efficiently with the summary view showing the changes at a glance. Filtered results can easily be exported to several CSV and HTML files for publication and/or result sharing with non-PEAKS users. Furthermore, results can be saved as a PEAKS project to be viewed by your collaborators with a free PEAKS Viewer.

De novo sequence tag generation

  • By specifying a confidence threshold with a user-friendly sliding bar, users can promptly convert the acclaimed PEAKS de novo sequencing results into high confidence de novo tags. Users can even export these tags for integration with their own in-house analysis workflow.

Improved inChorus search

  • The inChorus function combines the search results of several search engines, including Mascot 2.3. An intuitive search engine icon displays which specific engines identified each peptide and when multiple engines agree. The new filtration rule allows users to filter the results flexibly, including by individual engine scores. A Venn diagram and side-by-side FDR curves display each engine’s contribution to the final result.

Heatmap view of quantification results

  • The heatmap provides a bird’s-eye view of the protein quantity changes across different groups of samples. The proteins are automatically clustered according to their quantity change patterns, facilitating the quick identification of the possibly interesting proteins and patterns.

Heatmap view for LC-MS data

  • The data heatmap provides a bird’s-eye view of the peaks in the LC-MS data, with peptide features highlighted.

New statistical peptide score

  • The scoring function for evaluating peptide-spectrum matches is significantly improved in 5.3. This is the foundation of the increased accuracy and sensitivity of PEAKS DB. The scoring schema of peptide identification involves matched peaks and their intensities, precursor mass error, enzyme specificity, de novo sequence, peptide size, and more. A statistical evaluation, -10lgP, is given for each peptide-spectrum match. Here lg() is the common logarithm with base 10, and P is the probability that a false identification of the current search has the same or better significance.

Algorithm

  • Overall improvement of software capacity, stability and speed
  • Increased de novo and database search accuracy for ETD data
  • Automatic precursor mass and charge correction for high resolution data
  • Improved the SPIDER scoring function
  • Reduced the memory overhead for SPIDER, improving its capacity and speed
  • PTM support in manual de novo
  • Improved workflows targeting different application needs such as Identification, Quantification and inChorus
  • Replicate analysis for label free quantification
  • FASTA database validation, important for custom databases
  • CID/HCD, CID/PQD support in iTRAQ quantification with Thermo instruments
  • Improved support for Thermo LTQ RAW file format
  • mzML/mzXML3.0/mzData/pepXML file format support

Analysis

  • MCP compliant result exporting
  • Result comparison interface
  • Improved spectrum display
  • Standardized PTM display
  • Optional display of assigned/unassigned de novo peptides in PEAKS Search results
  • inChorus Search parameter saving
  • ndustry grade security and user management: System administrators can empower users and research groups to share resources without compromising security.
  • Efficient collaboration: Easily and automatically send/share results with clients/customers and coworkers.
  • 10% – 30% improvement in de novo sequencing accuracy on ion-trap data.
  • 11 instrument selection for maximum flexibility.
  • Improved charge and monoisotopic peak picking mean even better coverage.
  • New GUI design for optimal function and navigation.

Maximized User Privileges:

  • Individual user account, complete with password protection
  • Self-define individual databases, enzymes, post translational modifications
  • PPM support for parent mass error tolerance

Maximized Administrative Capabilities:

  • Ultimate control in defining user privileges
  • Configuration modifications are made easily in the GUI, instantaneously updated across the network.

New features

  • Taxonomy specific database queries with Swiss Prot will speed up the search times by narrowing the number of records that are compared and also narrowing the results to specific taxonomies.
  • The node task allocation has been optimized to increase individual cluster node performance. The optimization ensures that all the nodes are as busy as possible which increases overall cluster performance.
  • Data refinement has been incorporated with PEAKS Online. Charge recognition, low quality spectra filter and preprocessing functions have been added to get the most out of your data.
  • The result display now include the scan number and retention time if the data is present in the mzXML input file.
  • Any inputted zipped DTA file now have their names displayed in the results.

New features

  • Taxonomy specific database queries with NCBI NR will speed up the search times by narrowing the number of records that are compared and also narrowing the results to specific taxonomies.
  • User can define custom PTM’s to be used in an analysis.
  • The new “Peptide view” in the resulting .anz file can be used to sort the peptide results quickly and efficiently.

Performance enhancements

  • The protein ID search algorithm has improved scalability. A single task can contain tens of thousands of spectra.
  • The speed of the auto de novo and protein identification has been doubled. This means that the overall performance of Online is approximately 4 times faster.

Compatibility with earlier versions

  • The results and .anz files produced by PEAKS Online 1.0 are all compatible to the new results format found in PEAKS Online 1.1.

Bugs fixes since last release

  • The “outofboundary” exception bug that occurs when the client defined database is very small has been fixed.

Features

  • PEAKS Online is a cluster server with a web interface that allows multiple users to share data and processing power. This product has all the power of PEAKS Studio with the added benefit of a cluster server. A cluster server allows multiple PCs to work together on the same data set. This cuts processing time to a fraction of what it would take with one system doing all the work.
  • PEAKS Online has high availability. PEAKS Online is a web server for Peaks which means users can always use PEAKS Online, no matter where she/he is, as long as the user has internet connection and web browser.
  • Sharing your data results with trusted colleagues and clients is easy with the help of a browser and an internet connection.
  • The web interface is a single page that focuses on browsing and analysis options. Being so simple, users of the software can begin to analyze data and obtain meaningful results in no time.
  • PEAKS Online will send the results by email. The results are in both .html and .anz formats. The results were saved on the server so the user can always access the results as long as they are not deleted by the software administrator.
  • The result in the .html format can be sorted by m/z , sequence or score. (Note. only for data with less than 500 spectra because for big data it will take a very long time to load the page)
  • PEAKS Online has a task queue maintained on the database server. Users can always submit the tasks which will be put into the end of task queue automatically if the PEAKS Online server is busy with other task. Even the PEAKS Online server is down for some reason the task queue will not be destroyed or lose any task(s)
  • PEAKS Online can be configured to use one of several task schedule schemes. For example, heavy duty tasks can be scheduled to be processed during a certain time of the day only, which will make the server more responsive to normal sized tasks.
  • PEAKS Online offers a free online Mass Calculator for all PEAKS Online’s customers.

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