PEAKS
PEAKS Versions Page
The PEAKS product line has evolved rapidly from an auto de novo tool to a fully functional mass spectrometry
multi platform studio. Our past and present version features can be found here along with the proposed future features.
PEAKS Client and PEAKS Viewer's release notes are not included. PEAKS Viewer and PEAKS Client are released around the same time as PEAKS Studio, with the same version number. They are built with the same interface.
PEAKS Studio Versions
PEAKS Studio 4.5 - released July 2007
PEAKS Studio 4.2 - released November 2006
PEAKS Studio 4.0 SP1 - released August 2006
PEAKS Studio 4.0 - released July 2006
PEAKS Studio 3.1 - released November 2005
PEAKS Studio 3.0 - released June 6, 2005
PEAKS Studio 2.4 - released January 2005
PEAKS Studio 2.3 - released June 2004
PEAKS Studio 2.2 - released May 2004
PEAKS Studio 2.1 - released February 2004
PEAKS Studio 2.0 - released September 2003
PEAKS Online Versions
PEAKS Online 2.0 - released November 7, 2007
PEAKS Online 1.2 - released July 25, 2006
PEAKS Online 1.1 - released December 16, 2005
PEAKS Online 1.0 - released June 6, 2005
PEAKS Q Versions
PEAKS Q 1.0 - June 2006
Here is what we have bundled into PEAKS 4.5:
- 10% - 30% improvement in de novo sequencing accuracy on ion-trap data.
- Improvements to the inChorus search engine:
- Better integration with Sequest and Mascot - searches can be launched from inChorus, and/or existing results imported
- Existing results from any search engine can be loaded in (including PEAKS), avoiding having to repeat the search
- A separate local database is defined for recompiling the results based on peptides from all search engines
- The new RSD metric is available for all results, regardless of search engine
- Improvements to instrument flexibility
- Any combination of mass analyzer, fragmentation (incl. ETD) and ion source can be custom configured
- For ease of use, PEAKS will automatically check the data to detect the scan mode
- A new, revolutionary tool in SPIDER allows you to not only find homologous peptides, but also reconstruct the real sequence, confirming mutation and correcting de novo sequencing errors
- Retention time prediction: an RT is predicted for each peptide, and you can filter search results by (realRT – predictedRT)
- Data quality score now available, allowing a second evaluation of sequencing results trustworthyness
- All parameters (start to finish) plus user’s notes included on result export
- Improved charge and monoisotopic peak picking mean even better coverage
- Spectra can be exported to SVG, a standard graphics format, so you can move and resize parts of the picture
These are the things that our development team included in 4.2:
- Post analysis filtering -- results reports can be filtered by a number of criteria (for instance: score, delta mass, proteins with two good hits only, etc.)
- A simple report to summarize de novo sequencing on a whole run, will be included. It will look like 'peptide view'.
- The scans may now be sorted by scan number, mass, m/z, or retention time
- The de novo options screen allows users to limit the number of variable modifications allowed in a proposed de novo sequence.
-
Improved exporting:
- Images of spectra, spectra with ions annotated, sequence-spectrum alignment, ion tables and error plots can now be exported in high resolution for printing. The usability of the export utility is improved.
- WYSIWYG export of protein ID results, both from ‘peptide view’ and ‘protein view’ is enabled.
- SPIDER speed has been improved several fold; its accuracy has also been improved.
- Support for the HUPO organization’s proposed file format standard: mzData
PEAKS Studio 4.0 Service Pack 1
The following fixes and features are new in this service pack:
- SPIDER (Software Protein Identifier) is now available from a separate report in PEAKS. To assist in viewing the sequence tag matches and homology matches from the de novo sequences, a new addition to the search results report is presented -- a new pane in the peptide view showing the alignment between the sequence found in the database and the de novo sequence.
- Some errors have been corrected with regards to using the Data Refine tool on Thermo RAW data. RAW files that contain empty scans no longer cause troubles. Charge is recalculated from the spectral data where necessary, rather than relying on the scan header.
- Memory usege enhancements mean larger datasets can be processed. PEAKS writes search results to disk to free memory, and is more explicit in its memory management during processing
- Users can discover conserved regions in proteins, and easily distinguish between isoforms by way of a multiple sequence alignment tool. The new tool displays all matched peptides highlighted on the MSA. The MSA tool can be used on any number of proteins discovered after using PEAKS Protein ID, or inChorus protein ID.
- A small error has been corrected in the assisted manual sequencing tools. Users performing manual sequencing with modifications will find it easier to complete a sequence. Additionally, the pop-up menu items have been re-named for clarity.
- When configuring new databases, 'sticky folders' are used to make it easier to find the next file. As such, when you click the "browse..." button, the file chooser opens to the location of the last file you selected.
- When exporting Protein results to an .xls file or .html file from the Protein ID report, we launch Microsoft Excel or the default web browser, respectively, and open the report.
- The ion table can be configured by right clicking on it. One can now choose the number of decimal places to display, export, or switch between advanced and basic views.
- Improved performance for Swiss-Prot database "initialization for the purpose of taxonomy based searching".
The following new features are new in 4.0:
- Matrix Science Mascot and Thermo Sequest results can be viewed right along side of the PEAKS results. With both results side-by-side it is easier to quickly compare the findings. This new feature can be found in the "InChorus Database Search".
- SPIDER (Software Protein Identifier) is now part of PEAKS. This sequence tag based search tool confidently identifies peptides using the de novo sequences derived by PEAKS auto de novo sequencing. In addition to exact sequence tag search, SPIDER can identify peptides from the database that show significant homology to the de novo sequence. Find protein information even in unstudied organisms, or find sequence variation between samples. SPIDER differs from regular homology search tools in that it was designed to account for inherent de novo sequencing errors like: (I/L), (N/GG), (SAT/TAS).
- Thermo RAW data can be used directly without any conversion requirement. (XCalibur must be installed on the same computer).
- The PEAKS algorithm has been modified to take better advantage of FT and LTQ OrbiTrap high mass accuracy data.
- The Infochromics WIFF file data conversion tool can be plugged seamlessly into PEAKS Studio. Users with WIFF file data can now load and convert their data in one step.
- To get the most out of lower resolution data, a set of data refinement tools have been created. Users can now filter out spectra of insufficient quality, recover peptide charge state information, and merge scans of the same peptide.
- De novo and protein ID options panels have been reworked to provide better useability. Enzyme and PTM information is readily accessable and editable from the main screen. The whole parameter set can now be saved and easily recalled for future use.
- Taxonomy specific database queries with the Swiss-Prot database will speed up the search and improve the overall result quality by limiting the search to a smaller set of proteins.
The following new features have been incorporated with 3.1:
- Taxonomy specific database queries with NCBI NR will speed up the search and improve the overall result quality by limiting the search to a smaller set of proteins.
- The Mac and Linux versions will be released with most of the 3.0/3.1 functionality -- some 3rd party software that ships with PEAKS is unstable on MAC/Linux.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- The PEAKS algorithm has been rewriten for version 3.1 with a 70% increase in speed in protein ID and auto de novo sequencing!
- Consideration has been added for post-translational modifications (PTM) that occur only in the middle of a peptide.
- The new mzXML file loader is 10 times faster.
- De novo sequencing accuracy has been increased by 10%.
- Charge state is calculated from the mzXML MS/MS data that yields better sequence interpretation.
- The inChorus protein ID results give a more accurate confidence score by combining each protein search better.
- The MS/MS spectrum merging tool has been improved to account for a series of successive scans of the same peptide over a large retention time range.
Interface enhancements
The following enhancements to the user interface have been made for 3.0:
- If retention time is present in the input data, it is stored as a spectrum property and is reported.
Compatibility with earlier versions
PEAKS 3.1 will read .ANN files generated by all earlier releases of PEAKS, and is fully forward-and-backward compatible with PEAKS versions 2.1 through 2.4. Files generated by PEAKS 3.1 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions. ANZ files generated by PEAKS 3.1 can be read by prior versions of PEAKS, but only 3.0 can make use of inChorus protein ID results.
Bugs fixes since last release
- The XTandem Search part of the "inChorus" feature will not hang the analysis system if interrupted.
- Various small bugs will be fixed that cropped up from the 3.0 version.
New features
The following new features have been incorporated with 3.0:
- inChorus protein ID technology allows users to run and automatically combine the results from several protein identification tools (PEAKS, TANDEM, OMSSA). This approach has been proven to significantly improve the result quality and coverage.
- A high-throughput workflow creator makes processing several LC/MS/MS runs easy. Users can process a batch of data using whatever PEAKS tools they want.
- For FTMS instruments ECD mode is now fully supported. The Spectrum Alignment View now displays c-ion and z-ion series alignment.
- The Ion Table is now configurable to display any and all types of ions, 'basic' and 'advanced' defaults are provided.
- Users are now able to seemlessly open Micromass/Waters .RAW data in PEAKS.
- The ABI Converter, a data extraction tool for the ABI 4700 Oracle database has been developed, and now ships with PEAKS Studio. PEAKS Studio now reads the data files generated by the ABI Converter.
- BSI better supports the mzXML file format and now reads in mzXML scan number and mzXML retention time information.
- A 'Merge Spectra' tool has been added, allowing users to merge the MS/MS spectra of ions that represent the same peptide. This will reduce the amount of data to be processed, and improve its quality. Merging is dependent on similarity of precursor ion m/z, and retention time, if possible. Spectra may be merged only once, while loading, or after loading a data set.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- With the inChorus technology, protein identification quality and coverage is much improved.
- A new preprocessor has been developed for non-ion-trap data. As a result, users will see a 10% improvement in the results of auto de novo analysis on non-ion-trap data.
- Improvements have been made to the PEAKS protein identification tool's memory consumption.
Interface enhancements
The following enhancements to the user interface have been made for 3.0:
- A new reporting scheme has been implemented for use with inChorus protein ID. This shows the traditional protein report, plus a new peptide view - a sort-able list that tracks scan number, mass(calc), mass(exp), m/z, delta mass, sequence, protein accession, etc.
- The Spectrum Alignment View now displays c-ion and z-ion series alignment.
- he Ion Table is now configurable to display any and all types of ions, 'basic' and 'advanced' defaults are provided.
- Users may now choose to preprocess their data, or not.
Compatibility with earlier versions
PEAKS 3.0 will read .ANN files generated by all earlier releases of PEAKS, and is fully forward-and-backward compatible with PEAKS versions 2.1 through 2.4. ANZ files generated by PEAKS 3.0 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions. ANZ files generated by PEAKS 3.0 can be read by prior versions of PEAKS, but prior versions cannot make use of any inChorus protein ID results.
Bugs fixes since last release
- Some N-terminus peptide modifications could not be found. Fixed.
New features
The following new features have been incorporated with 2.4:
- Peaks has been fine tuned to take advantage of the superior accuracy and resolution provided by Fourier Transform (FTMS) instruments. CID, SORI, and IRMPD fragmentation modes are supported.
- BSI is proud to support the proposed mzXML file format standard and thus Peaks will now open these files.
- Peaks now records local time in the logging file to best assist technical support.
- HTML reporting has been implemented. Export in HTML format allows import into certain spreadsheeet programs for further analyses.
- A mass calculator tool has been added, enabling the researcher to quickly calculate the mass of a peptide, including modifications.
- A new report lists the spectra of quality not identified as part of a protein, and shows the de novo sequence found with each.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- The accuracy and the confidence level evaluation has been improved on PEAKS auto de novo to better reflect the quality of results. The above two improvements have drastically increased the number of correct sequences, tags and amino acids obtainable by PEAKS auto de novo. Also as a result of the above improvements, PEAKS 2.4 is slightly slower at de novo sequencing.
- Scalability of PEAKS Studio's Protein ID capabilities has been improved. The user will no longer run out of memory on large datasets (our tests run up to 6000 spectra and have found no problems so far).
- An error check has been added to the PTM editor. This lets the user know that the changes he/she is making to the current PTM.
Interface enhancements
The following enhancements to the user interface have been made for 2.4:
- A warning is shown when PEAKS fails to run because there is more than one copy running on a single machine.
- The export peptide sequence to .FAS format function now exports the same score as the one shown in PEAKS.
- The default spectrum and positional confidence colour scheme has been changed based on customer feedback.
- Users may now use keyboard shortcuts to navigate through the Protein ID report, and can now copy text with CTRL+C.
- The peptide sequences are now shown in Monospaced Sans Serif font: Lucidia Console.
Compatibility with earlier versions
PEAKS 2.3 will read .ANN files generated by all earlier releases of PEAKS, and is fully forward-and-backward compatible with PEAKS versions 2.1 through 2.3. ANN files generated by PEAKS 2.3 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions.
Bugs fixes since last release
- In the Peaks environment preference, color tab, the preview panel sometimes didn't display because of differing JRE support. Fixed.
- In the peptide data panel, drag and drop functionality (for example, creating a new node and drag-dropping some spectra there) failed. Fixed.
- In the peptide data panel, right clicking selected a spectrum (and deselected all other spectra). Fixed.
New features
The following new features have been incorporated with 2.3:
- The formula for computing protein ID confidence has been changed to better distinguish between high-scoring proteins. Proteins require 5 times as much evidence as peptides, so e.g. 5 peptides at 90% confidence each will produce 90% protein confidence, 10 peptides at 90% each or 5 peptides at 99% each will produce 99% protein confidence, etc. A 5% confidence threshold is applied to remove some of the least likely proteins and keep the report a reasonable size.
- PEAKS now correctly shows protein coverage information in the Protein ID result window. This coverage represents the number of amino acids found in sequence that match up to the sequence of the protein in question, and is expressed as a percentage of the length (in amino acids) of the whole protein sequence.
- Protein identification results can be accessed by clicking on "Protein ID Result" beneath the filename in the Peptide Data Frame. This is in addition to the current navigation method.
- The error tolerance input now allows free input, so you can experiment with high or low values for ion traps or FTMS (Note: for best results, use error tolerance values within the range 0.01 to 1.00 Da).
- The database configuration wizard now provides FTP download links directly, or copies the link to the clipboard at the user's choice.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- Speed and memory usage of Protein ID have been substantially improved.
Compatibility with earlier versions
PEAKS 2.3 will read .ANN files generated by all earlier releases of PEAKS, and is fully forward-and-backward compatible with PEAKS versions 2.1 through 2.3.
ANN files generated by PEAKS 2.3 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions.
Bugs fixes since last release
- In the Protein ID report, the protein coverage percentage has been corrected.
- The erroneous positional confidences are now computed correctly.
- Residues which are not present in the top scoring peptide may have non-zero positional confidence.
- In the presence of many transpositions in the top sequences, positional confidence may be higher.
- Protein ID uses the enzyme selected, and will no longer e.g. display non-tryptic results if tryptic digestion is selected.
- Sparse spectra with no significant peaks no longer produce errors.
New features
The following new features have been incorporated with 2.2:
- Support for MicroMass ProteinLynx XML format. PEAKS can now open and process these files.
- Peaks now shows protein coverage information in the Protein ID result window. This coverage represents the number of amino acids found in sequence that match up to the sequence of the protein in question, and is expressed as a percentage of the length (in amino acids) of the whole protein sequence.
- Protein identification results can be accessed by clicking a link in the main processing window of each spectrum. This is in addition to the current navigation method.
- UniProt database format support and download URL are now provided. This, as well as the IPI databases can be used for species specific studies (Mouse, Rat and Human).
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- Major improvements to the quality of protein ID from Ion Trap spectra.
- The number of proteins considered (internally) during database search has been increased - so as not to miss any protein candidates, and allowing more complex mixtures and larger numbers of redundant proteins in the database.
- Selecting the enzyme Arg-C (or similar enzymes) now selects a fragmentation pattern which better accounts for the possible presence of Lysine.
Compatibility with earlier versions
PEAKS 2.2 will read .ANN files generated by all earlier releases of PEAKS. .ANN files generated by PEAKS 2.2 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions.
Bugs fixes since last release
- Problems with manual sequencing commands have been resolved. Take special note of the repair to the search operations.
New features
The following new features have been incorporated with 2.1:
- The parameters that peaks uses to search a database and to perform auto de novo sequencing can now be defined separately. Also, database searching and auto de novo sequencing can be run independently of one another. The best practice is to perform de novo sequencing with only fixed PTM, then use variable PTM while searching the database.
- When installing PEAKS, the user may now choose a 768M memory size option.
- Any user-defined modifications found in sequence are saved in the .ANN file, for greater portability of results and if the user who doesn't have that modification on their local machine, it can be imported it into their local configuration.
- The "Database Configuration Wizard" assists in downloading configuring protein sequence databases so that protein ID result reports contain complete protein names and accesion numbers. The user may choose to apply any database's format to the results report. This can be selected during database configuration, or when viewing the report.
- Peaks can now load datafiles in XML format, facilitating data transfer from ProteinLynx Global Server.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- No major performance enhancements since last release.
Interface enhancements
The following enhancements to the user interface have been made for 2.1:
- Auto de novo and Protein Identification are given their own separate buttons.
- The user can choose to run the database search separately from de novo or subsequently.
- Independent parameters for each component are clearly presented / changeable.
- Complete database configuration wizard assists in downloading configuring protein sequence databases so that protein ID result reports contain complete protein names and accesion numbers.
Compatibility with earlier versions
PEAKS 2.1 will read .ANN files generated by all earlier releases of PEAKS. .ANN files generated by PEAKS 2.1 can be read by PEAKS 2.0, but PEAKS 2.0 cannot make use of any embedded post-translational modification definitions.
Bugs fixes since last release
- PEAKS no longer runs out of memory on certain datasets containing many unsequencable spectra.
New features
The following new features have been incorporated with 2.0:
- PEAKS provides protein identification. Peaks can now use its de novo sequence results to aid in database searching and protein identification.
- Wizards are provided to help users configure PEAKS.
- PEAKS allows for differences in the quality of data between instruments. PEAKS now supports ion trap data.
Performance enhancements
The following enhancements have in added into the PEAKS algorithm:
- Major accuracy improvement when sequencing using ion trap data.
- Major accuracy improvement when sequencing non-tryptic peptides.
Compatibility with earlier versions
PEAKS 2.0 will read .ANN files generated by all earlier releases of PEAKS. PEAKS 2.0 .ANN files can be read by 1.x, but will lose any protein id information.
Bugs fixes since last release
- Numerous minor bugs have been fixed.
New features
The shared resource for high throughput processing server/cluster solution now provides:
- Industry 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
The following new features have been incorporated with 1.2:
- 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
The following new features have been incorporated with 1.1:
- 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 following enhancements have in added into the PEAKS Online algorithm:
- The protein ID search algorithm has improved scalablity. 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 compatiable 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
The following features have been incorporated with 1.0:
- 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 availablity. 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.
Features
The following features have been incorporated with 1.0:
- PEAKS Q is a quantitation software that finds protein ratios from MS/MS data between control and experimental protein samples
- Both ICAT and SILAC labeling techniques can be processed by this first, free version of PEAKS Q
- Custom quantification labels can be created to allow for alternative labeling techniques
- Custom enzyme and PTM sets can be created and used with PEAKS Q's build protein search engine.
- The interactive display and zoom capabilities allow the user to inspect the results visually.
- The results "Peptide abundance ratio calculation" graph depicts the heavy (red) and light (blue) peptide pair ratio when a particular peptide is highlighted. When no peptide is selected the graph shows the overall heavy/light protein ratio
- The "Task" view shows the user at what point the software is in analyzing the data.
