Wednesday, May 21, 2014
PEAKS Two Day Workshop, June 24 - 25, 2014 - Boston, MA, USA
The PEAKS team will host a two-day workshop at Hilton Boston Back Bay Hotel in Boston. The early bird registration is open until May 31. You can register the workshop here.
Tuesday, May 13, 2014
Annual PEAKS User Meeting co-located with ASMS 2014
It is the time of the year again to get prepared for the ASMS conference. We are happy to announce that the 8th Annual PEAKS User Meeting will take place on June 15, 2014, co-located with ASMS.
Please join us and register today to reserve your seat. http://www.bioinfor.com/peaks/corp/conferences/peaks-asms-2014.html
This year, the user meeting will focus on PEAKS applications. Both the guest speakers and scientists from the PEAKS team will talk about real research and how PEAKS may help in the process. We have reserved the room for the entire afternoon. So if you want to discuss how PEAKS may help on your research project, you are welcome to talk to our scientists individually after the user meeting.
If you cannot make it to the user meeting, please do visit us at our booth (#42).
See you in Baltimore!
Please join us and register today to reserve your seat. http://www.bioinfor.com/peaks/corp/conferences/peaks-asms-2014.html
This year, the user meeting will focus on PEAKS applications. Both the guest speakers and scientists from the PEAKS team will talk about real research and how PEAKS may help in the process. We have reserved the room for the entire afternoon. So if you want to discuss how PEAKS may help on your research project, you are welcome to talk to our scientists individually after the user meeting.
If you cannot make it to the user meeting, please do visit us at our booth (#42).
See you in Baltimore!
Monday, April 28, 2014
PEAKS 7 Patch Release
While laying down the foundation of the next major upgrade, we are also improving the current version. Just a few weeks ago, the PEAKS team has released a new build of PEAKS 7 to address some issues in the 2013 November release.
If your PEAKS 7 installation works well for you, you do not need to upgrade to the new build. Here are a list of changes in the new build.
If your PEAKS 7 installation works well for you, you do not need to upgrade to the new build. Here are a list of changes in the new build.
- Improved 3rd party exporting to Scaffold and fixed an issue that sometimes the PTM information may be missing
- Fixed an issue that sometimes the proteins reported in mzIdentML does not have supporting peptides
- 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 support 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
- PEAKS 7 will now less likely to exit shortly after the start up due to the slow Derby initialization on some system. The default timeout has been increased to 30 seconds
- PEAKS project converter. Now the MS1 spectrum information is correctly converted from PEAKS 6 projects
Tuesday, March 4, 2014
Using PEAKS via Windows Remote Desktop Connection
Recently some users reported an graphics issue when using PEAKS over Windows remote desktop connection. PEAKS GUI is not drawn correctly on the screen.
We have observed the same issue in the team internally and investigations lead us to believe the issue resides in Java Windows look and feel. I did some internal testing and it seems using the cross-platform look and feel solved the problem.
To make things easier for you, here is a modified jar file you can use to replace peaksstudio.jar in the PEAKS directory. Your PEAKS build number (go to Help -> About PEAKS to check) must match the build number of the jar, e.g. build 20131119. Please make sure you backup your original peaksstudio.jar just in case.
To make things easier for you, here is a modified jar file you can use to replace peaksstudio.jar in the PEAKS directory. Your PEAKS build number (go to Help -> About PEAKS to check) must match the build number of the jar, e.g. build 20131119. Please make sure you backup your original peaksstudio.jar just in case.
Thursday, February 13, 2014
Create complex projects with ease in PEAKS 7
One of the issues in previous version of PEAKS is the difficulty on creating large, multiple sample projects. Users have to make hundreds of mouse clicks to create a project with hundreds of samples.
Introduced in PEAKS 7, the new project wizard has all the functionality in the previous versions and provides additional controls to make creating complex project easily. You can still use the new project wizard the exact same way as it is in the previous version to quickly create simple projects containing only a few fractions and samples.
Below is a screenshot of the new project wizard interface. The portion in the red rectangle is the new controls introduced in PEAKS 7. It essentially provides a staging area for all related data files, a search function to help quickly highlighting multiple files and control buttons to add the highlighted files to the project in different ways.
You can use the "Add Data" button to add data files to the staging area. The files will be listed in the white box on the left. Once the files are listed there, you can then type a few characters in the search box to highlight files of interest. PEAKS will gray out the files that do not match the search and pull all the matched files to the beginning of the list.
Once you have one or multiple files selected in the staging area, you can use one of the three buttons to add them into the project.
The first button will create a new sample and put all the selected files under the new sample as fractions. This is equivalent to adding multiple files to one sample in the old way. The second button will create a new sample for each selected files. This is very useful when creating a PEAKS project with hundreds of samples. The third button is to be used to add more fractions into an existing sample. The forth button is to be used to remove samples and/or fractions from the project.
The new project wizard also integrated the most commonly used analytical workflow in PEAKS, starting from data refinement (data pre-processing) to peptide/protein identification, including PTM analysis and mutations. The workflow may include label free quantification if the context is applicable.
Introduced in PEAKS 7, the new project wizard has all the functionality in the previous versions and provides additional controls to make creating complex project easily. You can still use the new project wizard the exact same way as it is in the previous version to quickly create simple projects containing only a few fractions and samples.
Below is a screenshot of the new project wizard interface. The portion in the red rectangle is the new controls introduced in PEAKS 7. It essentially provides a staging area for all related data files, a search function to help quickly highlighting multiple files and control buttons to add the highlighted files to the project in different ways.
You can use the "Add Data" button to add data files to the staging area. The files will be listed in the white box on the left. Once the files are listed there, you can then type a few characters in the search box to highlight files of interest. PEAKS will gray out the files that do not match the search and pull all the matched files to the beginning of the list.
Once you have one or multiple files selected in the staging area, you can use one of the three buttons to add them into the project.
The first button will create a new sample and put all the selected files under the new sample as fractions. This is equivalent to adding multiple files to one sample in the old way. The second button will create a new sample for each selected files. This is very useful when creating a PEAKS project with hundreds of samples. The third button is to be used to add more fractions into an existing sample. The forth button is to be used to remove samples and/or fractions from the project.
The new project wizard also integrated the most commonly used analytical workflow in PEAKS, starting from data refinement (data pre-processing) to peptide/protein identification, including PTM analysis and mutations. The workflow may include label free quantification if the context is applicable.
Thursday, January 30, 2014
PEAKS 7 Viewer on Mac OS X Mavericks
I wrote a post in early 2013 here to help users to run PEAKS as a Viewer on Mac OS or Linux. Similar procedure applies to PEAKS 7 as well. Many thanks to user ceinwyn that brought the issue to me that PEAKS DB search results cannot be opened.
I spent some spare time looking into this issue and luckily found a workaround. Just want to re-state my disclaimer here.
Disclaimer: PEAKS does not officially support any OS other than Windows as of the time I am writing the post. The software may not be fully functional. Activating the software on OS X or Linux will consume the license, which means the same license can not be used again. I strongly recommend only following the steps to configure PEAKS Viewer (the unlicensed Studio) on OS X or Linux for PEAKS result sharing and presentation purposes.
Basically what happened here is that PEAKS 7 has some sizing issue with the Auqa look and feel from Apple Mac OS X. The workaround is to change the look and feel to a cross-platform one that Apple also support. To make things easier, I have put a modified version of the jar file here. And here are the steps:
Enjoy PEAKS and happy sharing!
I spent some spare time looking into this issue and luckily found a workaround. Just want to re-state my disclaimer here.
Disclaimer: PEAKS does not officially support any OS other than Windows as of the time I am writing the post. The software may not be fully functional. Activating the software on OS X or Linux will consume the license, which means the same license can not be used again. I strongly recommend only following the steps to configure PEAKS Viewer (the unlicensed Studio) on OS X or Linux for PEAKS result sharing and presentation purposes.
Basically what happened here is that PEAKS 7 has some sizing issue with the Auqa look and feel from Apple Mac OS X. The workaround is to change the look and feel to a cross-platform one that Apple also support. To make things easier, I have put a modified version of the jar file here. And here are the steps:
- Check the version of PEAKS. Go to Help -> About PEAKS. In the dialog, you should see the build number, e.g. build 20131119. This build number must match the number in the downloaded jar file in the above link.
- Close PEAKS.
- Download the jar file and replace the peaksstudio.jar in the PEAKS directory with this one.
- Start PEAKS and now the PEAKS DB search results can be opened.
Enjoy PEAKS and happy sharing!
Thursday, January 9, 2014
De Novo Sequencing using Spectral Pairs or Triplets
PEAKS supports de novo sequencing using spectral pairs or triplets that are generated using different fragmentations. This is a feature introduced in PEAKS 7. Here is the poster that briefly described the method.
To use this function, simply specify the fragmentation mode as 'Mixed' during project creation, PEAKS will then automatically detect spectral pairs or triplets when doing de novo sequencing.
There are a few things to watch out though. When the fragmentation mode is set to 'Mixed', PEAKS will try to get this information from the data for each individual spectra. From the many datasets we have tested, this is generally not a problem for Thermo raw files. Other formats, especially some in-house generated XML files(e.g. mzXML, mzML) may be problematic as they either do not include the fragmentation mode information at all or PEAKS won't be able to retrieve the information for various reasons. In this case, PEAKS will ignore those spectrum, thus generating empty de novo sequencing results.
When the fragmentation mode information is available, the spectral pairs or triplets will be formed if the spectrum are from the same precursor ion in the same MS scan. The de novo sequencing result from a pair or triplet will be presented in a single row in the peptide table. The spectrum annotations for different fragmentation mode will be stacked vertically on the screen.
If you click the 'All candidates' button, all the calculated de novo sequences will be displayed in a pop up window. You can then click on those sequences to examine the spectrum annotation from individual fragmentation mode.
In the above example, although PEAKS has figured out the correct sequence using any one of the fragmentation mode, the confidence of the sequence from the triplet is much better.
To use this function, simply specify the fragmentation mode as 'Mixed' during project creation, PEAKS will then automatically detect spectral pairs or triplets when doing de novo sequencing.
There are a few things to watch out though. When the fragmentation mode is set to 'Mixed', PEAKS will try to get this information from the data for each individual spectra. From the many datasets we have tested, this is generally not a problem for Thermo raw files. Other formats, especially some in-house generated XML files(e.g. mzXML, mzML) may be problematic as they either do not include the fragmentation mode information at all or PEAKS won't be able to retrieve the information for various reasons. In this case, PEAKS will ignore those spectrum, thus generating empty de novo sequencing results.
When the fragmentation mode information is available, the spectral pairs or triplets will be formed if the spectrum are from the same precursor ion in the same MS scan. The de novo sequencing result from a pair or triplet will be presented in a single row in the peptide table. The spectrum annotations for different fragmentation mode will be stacked vertically on the screen.
If you click the 'All candidates' button, all the calculated de novo sequences will be displayed in a pop up window. You can then click on those sequences to examine the spectrum annotation from individual fragmentation mode.
In the above example, although PEAKS has figured out the correct sequence using any one of the fragmentation mode, the confidence of the sequence from the triplet is much better.
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