PEAKS Frequently Asked Questions

Question: How do I install PEAKS Studio 5.1 (with internet)?

Question: How do I install PEAKS Studio 5.1 (without internet)?

Question: What is the required system configuration for PEAKS?

Question: What enzymes should I use to digest the protein, in order to use PEAKS to interpret the MS/MS data?

Question: Why can I not find the freeze bar to indicate the position of the peak in the ion edit window when I select an ion in the ion table?

Question: Where can I get the log file for PEAKS?

Question: What are the differences between PEAKS and other de novo sequencing programs?

Question: I'd like to use my own private protein database. How should I format the header so that PEAKS will accept it?

Question: The mass shown in brackets during manual sequencing -- e.g. [1407.21] -- does not seem to be a proper molecular weight. Why?

Question: How do I configure Mascot?

Question: How do I configure Sequest?

Question: Why do my results not show up in the main window, even though it shows up in the Project View?

Question: I can’t seem to open my ABI (.wiff)/ Bruker/Shimadzu/Varian file. What can I do?

Question: How can I change my memory heap size for Java so that Peaks has more memory to use?

Question: How do I do manual de novo sequencing?

Question: How can I save my results/project?

Question: How can I change my default output directory?

Question: How can I convert my PEAKS 5.0 project files and view them in PEAKS 5.1

Question: Why are protein ID/de novo/other functions buttons grayed out?

Question: What does "-1" mean in my iTRAQ/SILAC results?

Question: Why can’t I perform label free quantification?

Question: How can I use 3D View?

Question: I just did ICAT/iTRAQ/SILAC (any quantification except for label free) but do not see any results. Where are the results?

Question: How is the peptide score calculated?

Question: How is a protein score calculated?

Question: How do I register PEAKS Studio 5.1 (with internet)?

Answer. The first time PEAKS is run, the license wizard will appear automatically. From here, there are 2 options: registration with and without an internet connection. Select the first option, request license file (has internet connection). Click “Next”. Enter the necessary registration information. The email address entered here will be used to send you a license file, different from a registration key. If you have purchased PEAKS and have a registration key, looks like PS*************, enter/paste this into the respective field, careful not to include any spaces. For those evaluating the software, request a license file by entering your instution's name in the corresponding lower field. Click "Next". An automated BSI service will generate the license file (license.lcs) and email it to the provided email account from the License Wizard. You can either save the attachment to a local directory or copy the content between '===>' and '<===' in the email, then paste it into this page. Click “Next”. If all has been followed correctly, a message that the license has been imported successfully will appear. Click finish and restart PEAKS. For deeper explanation, images and other methods, please consult the PEAKS User's Manual, Chapter 2, section 4.1.

Question: How do I register PEAKS Studio 5.1 (without internet)?

Answer. The first time PEAKS is run, the license wizard will appear automatically. From here, there are 2 options: registration with and without an internet connection. Select the second option, request license file (without internet connection). Click “Next”. Enter the necessary registration information. The email address entered here will eventually be used to send you a license file, different from a registration key. If you have purchased PEAKS and have a registration key, looks like PS*************, enter/paste this into the respective field, careful not to include any spaces. For those evaluating the software, request a license file by entering your instution's name in the corresponding lower field. Click "Next". The window now offers the opportunity to "Save Request File" to our computer, by clicking on the button. Once saved, click "Next". Transfer the license request file from this PC to another PC which does have an internet connection, perhaps via USB key or another removable storage device. Using the PC with internet connection, logon to http://www.bioinfor.com/lcs20. Select “I have the license request file. I want to register the software” and click “Next”. Click the “Browse” button to select the license.request file, type in the visual verification code and click “Next”. An automated BSI service will generate the license file (license.lcs) and email it to the provided email account entered from before. After the license email is received on the PC with internet connection, save the attachment, license.lcs, as is and copy the file to the computer without an internet connection. If you do not receive the license.lcs file in your inbox, please check your junk mail folder. In the license wizard on the computer without an internet connection, click the 'Browse' button below to select the license.lcs file and click “Next”. If all has been followed correctly, a message that the license has been imported successfully will appear. Click finish and restart PEAKS. For deeper explanation, images and other methods, please consult the PEAKS User's Manual, Chapter 2, section 4.2.

Question: What is the required system configuration for PEAKS?

Answer. PEAKS can be run on any computer that supports Sun's Java Runtime Environment (JRE) 1.4 (or JRE 1.5 for PEAKS Studio 4.0 or later). On installation, PEAKS will install a dedicated JRE for its use, so it can co-exist with another version of Java on our machine. The system should also have: 1-2Gb RAM, 1GB free space on hard drive (more for mass spec data and results), an AMD or Intel 2GHz CPU. The minimum configuration is 1GB of RAM and 1Ghz CPU, but we recommend 1.5GB of RAM.

Question: What enzymes should I use to digest the protein, in order to use PEAKS to interpret the MS/MS data?

Answer. The most popular enzyme for digesting proteins for MS/MS analysis is trypsin. PEAKS comes with an AAs/PTMs set, predefined for unmodified tryptic digests, to handle this common case. Tryptic peptides typically show excellent MS/MS spectra, and produce good sequences. If you wish to use a different enzyme, or sequence small peptides in entirety, you can create a new AAs/PTMs set and select another enzyme. Selecting an ‘unknown enzyme’ places no restrictions on the residues appearing at the C-terminal end. You may set them yourself.

Question: Why can I not find the freeze bar to indicate the position of the peak in the ion edit window when I select an ion in the ion table?

Answer. The spectrum is zoomed in to far, or not in the right area. Adjust your spectrum view’s zoom to 1:1.

Question: Where can I get the log file for PEAKS?

Answer. The log file can offer us some information for bug tracking. PEAKS sets the location of the log and configuration file, users can not change it. Its location is listed under Preferences, in the General section. Usually it's in c:\documents and settings\#username#\.peaks\PEAKSLOG_#.txt

Question: What are the differences between PEAKS and other de novo sequencing programs?

Answer. Bottom line: result quality. PEAKS consistently gives more accurate peptide sequences and with better confidence than other programs. This is a result of PEAKS' global optimization algorithms and sophisticated scoring schema.

Question: I'd like to use my own private protein database. How should I format the header so that PEAKS will accept it?

Answer. PEAKS does not have many special requirements for a database. It must be in FASTA format, and the header should contain only standard ASCII characters.

Question: The mass shown in brackets during manual sequencing -- e.g. [1407.21] -- does not seem to be a proper molecular weight. Why?

Answer. The [1407.21] is not a molecular weight, it is less than the molecular weight (with the difference being, say, the mass of water). This is because the [1407.21] represents only the mass of the remaining amino acid residues that PEAKS must assign.

Question: How do I configure Mascot for PEAKS inChorus?

Answer. It's quite easy to configure PEAKS and Mascot, just open up Preferences -> Search Engines -> Mascot. In this window you will tell PEAKS how to access your Mascot server (if applicable). Enter the Host name (or an IP address), Port, Virtual Directory as well as your user name, password and email address. To make sure that you entered everything correctly and that the server is working, click the “Test Connection” button. If you would like to save your password so that you don’t have to enter it every time, check the “Save Password” box. Click the “Apply” button to save any changes you have made. In the event that Mascot is installed on the local computer, type "localhost" in the Hostname (or IP address) field.

Question: How do I configure Sequest for PEAKS inChorus?

Answer. It's not that difficult to do, just open up Preferences -> Search Engines -> Sequest. To use Sequest click the “Browse” button to tell PEAKS where to find the search engine. You must also browse your computer to find the location of the “Default Sequest Parameter File (.params)” as well as the “Sequest Result Output Folder”. Click the “Apply” button to save any changes you have made.

Question: Why do my results not show up in the main window, even though it shows up in the Project View?

Answer. To view results, double click on the node in the Project View.

Question: I can’t seem to open my ABI (.wiff)/ Bruker/Shimadzu/Varian file. What can I do?

Answer. First make sure the correct version of the instrument vendor's software (i.e. Analyst, CompassXport) is installed in same computer as PEAKS. Next, check the file settings in PEAKS under Preferences, under the Instrument section.

Question: How can I change my memory heap size for Java so that PEAKS has more memory to use?

Answer. The default of 1024 MB tells the Java Virtual Memory (which runs PEAKS) to run with 1024 MB of memory. To increase the JVM and determine the highest optimal value for your own computer. Click the "Memory Utility" icon, found in your installation directory. Often the Start Menu will host this feature, with the other PEAKS applications. Once the window is open, in the designated field, enter the prefered settings, then hit Apply. Some trial and error may be needed as Java will not start if you set the value to be too large for your system.

Question: How do I do manual de novo sequencing?

Answer. PEAKS 5.1 provides a set of tools to help you sequence a peptide, using graphic cues from the spectrum. Visit section 6.3 in the User's Manual for a thourough description of Manual De novo Sequencing.

Question: How can I save my results/project?

Answer. Easy. Everything is saved automatically!

Question: How can I change my default output directory?

Answer. The database structure for PEAKS is now constructed using a derbyServer and serverDB folders. If you prefer to change the default location, select Preferences -> General. From here, simply use the Browse tool too naviate to the desired location for each option. Please note that the Project folder, must be located withing the derby sercer folder; ie. derbyServer/serverDB. Once complete, select "Apply" before clicking "OK"

Question: How can I convert my PEAKS 5.0 project files and view them in PEAKS 5.1?

Answer. Projects created using PEAKS 5.0 are different than those produced with 5.1. PEAKS provides a straight-forward project conversion tool that will allow users to quickly enhance existing projects to be supported in PEAKS 5.1. Users comfortable with command line, will find the tool very easy. This section will cater to those unfamiliar with command line, but who wish to convert their necessary projects promptly. There are two main methods that can be used to generate a PEAKS 5.1 project from an existing 5.0 project. The first method converts a 5.0 project and stores the 5.1 project in the same directory as the original file, with the addition of “51” to the end of the file. Just enter ProjectConverter followed by the PEAKS 5.0 project location and name. For example, if the project is found in your C:\PeaksStudio5.0\derbyServer\serverDB\My5.0Project folder, enter: ProjectConverter “C:\PeaksStudio5.0\derbyServer\serverDB\My5.0Project”. This will produce a new 5.1 project in this same directory, with the name "My5.0Project.51." The quotation marks (“) surrounding the location are not necessary in this case, but are necessary if your path contains any spaces, such would be found in use of “C:/My Documents/Projects…”. 2. To produce a new file in a different directory, the only change is the addition of leaving a blank space, and then entering the output directory, such as “C:\PeaksStudio5.1\derbyServer\serverDB\My5.1Project”. Thus the line will look like: ProjectConverter “C:\PeaksStudio5.0\derbyServer\serverDB\My5.0Project” “C:\PeaksStudio5.1\derbyServer\serverDB\My5.1Project”. If the new directory does not already exist, the program will create the directory for you. If the directory already exists, entering a dash and the letter ‘-f’ before the original project will force the ProjectConverter to overwrite any existing projects in this location.For example: ProjectConverter -f “C:\PeaksStudio5.0\derbyServer\serverDB\My5.0Project” or ProjectConverter -f “C:\PeaksStudio5.0\derbyServer\serverDB\My5.0Project” “C:\PeaksStudio5.1\derbyServer\serverDB\My5.1Project”. You are now ready to call up these projects into PEAKS 5.1.

Question: Why are protein ID/de novo/other functions buttons grayed out?

Answer. This could depend on which result node in the Project View is highlighted. For example, if you have a protein ID result selected, you can select SPIDER, PTM finder etc. Essentially, these grayed out features act as a comment to users to be aware of the node currently selected.

Question: What does "-1" mean in my iTRAQ/SILAC results?

Answer. "-1" means that a ratio was found but it was not derived from a high scoring peptide. If you want the ratio to be counted you can change the minimum and maximum scores of a peptide that are included in the ratio calculation.

Question: Why can’t I perform label free quantification?

Answer. The most likely reason is users to have at least two samples, the same number of fractions in each sample. Also, label free quantification works best if label free quantification is performed on the combined protein ID results of all the samples

Question: How can I use 3D View?

Answer. As this may be considered an advanced monitor feature, the 3D View may only work for computers that have newer video cards. If it is turned on for an older computer, it may cause a JVM crash, resulting in PEAKS shuting down. For computers with the necessary hardware, the feature to turn on and off the 3D View can be found in Prefernces -> Performance. When the tick box has a check mark inside, the 3D View is enabled; when it is clear, the 3D View is disabled.

Question: I just did ICAT/iTRAQ/SILAC (any quantification except for label free) but do not see any results. Where are the results?

Answer. For user convenience, the results are grouped with the protein ID results. Once the quantification data has been amalgomated with the protein ID results, the Project View node corresponding to the data's icon will change to have a little Q at its base.

Question:How is the peptide score calculated?

Answer. The peptide score reported in PEAKS 5.2 is a probability score. The basic idea to compute a probability score for a peptide-spectrum match is to compute a probability conditioned on some features which can distinguish correct matches from false ones. A more detailed answer can be found in this document: Peptide Score Decription.

Question:How is a protein score calculated?

Answer.. The protein score in PEAKS (database search) is the sum of the supporting peptide scores for each distinct sequence. That is, excluding the scores of duplicate matches. A more detailed answer can be found in this document: PEAKS Protein Scores.