PEAKS will be in Paris, France hosting both a training course and a workshop starting this September.
A two-day PEAKS training course and a one-day workshop will be held at the Hotel Paris Bastille located at 67 rue de Lyon, Paris France.
The training course is designed to introduce users to the software, and elevate their understanding to become a confident user. Attendees will gain hands-on data analysis experience with PEAKS from the people who develop and support it.
The workshop is designed for participants facing more difficult challenges in their research. This hands-on PEAKS practice will definitely increase your expertise of LC-MS/MS data analysis and quality control.
More details can be found here. You can also register here directly.
Thursday, July 31, 2014
Tuesday, June 24, 2014
BSI Joins Battle to End Cancer in our Lifetime
On the weekend of June 7th and 8th Bioinformatics Solutions Inc, makers of PEAKS software, was happy to sponsor one of its team members Dan Maloney in the Ontario Ride to Conquer Cancer. It was a grueling two day 235 km ride from downtown Toronto to the top of Niagara Falls. Through personal donations from friends, family, and co-workers, and a $1500 sponsorship from BSI, Dan was able to raise over $2500 to support the Princess Margaret Cancer Foundation. Over 5000 riders participated in the event. Together they were able to raise over $20 million to fund cutting edge cancer research. This amazing achievement is a new fundraising record for the ride and we are happy to have played a part.
The Princess Margaret Hospital's research program is ranked fourth in the world. That is in terms of the percentage of publications cited in high impact oncology journals. It is the research center where important discoveries such as Dr. James Till and Dr. Ernest McCulloch’s discovery of stem cells in 1961 were made. Currently, they are pushing forward to improve the effectiveness of personalized medicine in the fight against cancer. Also, one of their researchers, Dr. Tak Mak, has recently received Health Canada and FDA approval to go ahead to phase 1 clinical trials for a new cancer drug that will target PLK4, an important enzyme in cancer cell division. We are happy to support research such as this happening at Princess Margaret to help end a disease that 2 out of 5 Canadians will be diagnosed with in their lifetime.
When asked about the ride Dan Maloney said, "it was a very rewarding experience, but I was overjoyed to cross the finish line. Thank you very much to everyone who was able to make a donation. Very special thanks to BSI for sponsoring me. Without generous donations like the one you made, large fundraising events such as this would not be possible. Events such as the Ride to Conquer Cancer are crucial if we ever want to see the end of devastating diseases such as cancer which sadly will affect us or someone we love at some point in our lives."
The Princess Margaret Hospital's research program is ranked fourth in the world. That is in terms of the percentage of publications cited in high impact oncology journals. It is the research center where important discoveries such as Dr. James Till and Dr. Ernest McCulloch’s discovery of stem cells in 1961 were made. Currently, they are pushing forward to improve the effectiveness of personalized medicine in the fight against cancer. Also, one of their researchers, Dr. Tak Mak, has recently received Health Canada and FDA approval to go ahead to phase 1 clinical trials for a new cancer drug that will target PLK4, an important enzyme in cancer cell division. We are happy to support research such as this happening at Princess Margaret to help end a disease that 2 out of 5 Canadians will be diagnosed with in their lifetime.
When asked about the ride Dan Maloney said, "it was a very rewarding experience, but I was overjoyed to cross the finish line. Thank you very much to everyone who was able to make a donation. Very special thanks to BSI for sponsoring me. Without generous donations like the one you made, large fundraising events such as this would not be possible. Events such as the Ride to Conquer Cancer are crucial if we ever want to see the end of devastating diseases such as cancer which sadly will affect us or someone we love at some point in our lives."
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.
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