PEAKS Frequently Asked Questions

Question: What is .ANN format?

Question: What is the required system configuration for PEAKS?

Question: I started an auto de novo process / protein id, but nothing happened. What did I do wrong?

Question:Can I edit the data file manually in PEAKS?

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

Question: Can I edit/modify the result of PEAKS Auto De novo?

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: How can I save the sequences resulting from auto de novo?

Question: We saw a triangle on the m/z axis of the spectrum. What does that represent?

Question: How can I stop a task from running?

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

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

Question: Database search (for protein identification) will not run, and is grayed out in the Auto De Novo Properties dialogue, how do I make PEAKS perform database searching?

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

Question: When searching a database (to identify my protein) against my non-tryptic digest sample, I get an out of memory error. What did I do wrong?

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

Question: What is the required system configuration for MAC?

Question: Can the linux version run on any version of linux?

Question: How do I configure Mascot?

Question: How do I configure Sequest?

Question: How do I install PEAKS on a computer running Windows Vista?

Question: How do I install PEAKS on a computer without Internet access?

Question: What is the .ANZ file format?

Answer. This is PEAKS native file format. It contains data and results in zip compressed XML format. If you open an ANZ file with winzip, you can see an ANN index file and a folder with ANN data files (both of them use the same extension ‘ann’). Each ANN data file contains the MS/MS information and peptide information from one spectrum. An ANN index file can be used to organize multiple spectra. The ANN index file links to a directory that contains multiple ANN data files.

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.

Question: I started an auto de novo process / protein id, but nothing happened. What did I do wrong?

Answer. First, check the Tools menu and verify that Enable Tasks Running is checked. If it is disabled, the ‘Task Queue’ will be shown in red and no tasks in the queue will be processed. It is possible that the process is running but you just don’t notice. PEAKS processes the auto de novo task in the background so you can continue to work. This process takes several seconds. You will find the job is still in the queue if you check the Task Queue Frame. After the process is done, it will disappear from the queue. By selecting the spectrum in the Peptide Data Frame, you can find the peptide candidates, the spectrum image and ion alignment in the main process window.

Question: Can I edit the data file manually in PEAKS?

Answer. You can edit the precursor information (m/z and charge) by right clicking on the precursor in the Peptide Data Frame. However, you cannot edit the spectrum data itself from within PEAKS.

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: Can I edit/modify the result of PEAKS Auto De novo?

Answer. You cannot modify the sequences returned by PEAKS Auto De Novo search. However, you can copy the sequence for manual de novo to achieve the same goal. Right-click on the desired sequence and select Copy for manual de novo. You can now edit the sequence and ion assignments in the Manual De Novo section of the Peptide Candidates tree.

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: How can I save the sequences resulting from auto de novo?

Answer. There are a number of ways to export them. If you're looking for a tabular output, try File -> export -> HTML. If you're looking for an image of the spectrum, try right-clicking on the spectrum. The user's manual contains more complete help on this subject.

Question: We saw a triangle just under the m/z axis of the spectrum. What does that represent?

Answer. This green triangle is used to shown the location of the precursor ion (with charge 1).

Question: How do I stop a task from running?

Answer. Right-click the task in the Task Queue. From the popup menu, choose “remove”.

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 in the Environment Configuration Dialoged, under the Environment tab. Usually it's in c:\documents and settings\#username#\.peaks\peaks.log

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: When searching a database (to identify my protein) against my non-tryptic digest sample, I get an out of memory error. What did I do wrong?

Answer. PEAKS Studio has limitations on the number of spectra that can be run without running into memory limitations -- around 10000 spectra. We are working on scalability, but for now, try splitting your data up into chunks.

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: What is the required system configuration for MAC?

Answer. The system should also have: 1-2Gb RAM, 1GB free space on hard drive (more for mass spec data and results), and a 1.5Ghz PowerPC G4 processor. The minimum configuration is 512Mb of RAM and 867Mhz G4 CPU.

Question: Can the linux version run on any version of linux?

Answer. Any version of linux that will support Java 1.5 is exceptable. Java need not be installed on the linux system before the PEAKS installation. PEAKS has all the necessary Java components it requires in its installer.

Question: How do I configure Mascot for PEAKS inChorus?

Answer. It's quite easy to configure PEAKS and Mascot, just open up Edit -> Configuration -> Environment Preferences and go to the Search Engines tab. Once there, you just have to type in the location of your server. The only difficult part is knowing where your server is. We recommend just asking your IT person, or the person who set up the server. Note that you usually don't have to worry about preceding or trailing slashes. You can use your regular user account for the username and password. It doesn't necessarily have to be an administrator account. However, some of the built in user accounts like 'daemon' have some special properties that cause problems here. Don't use the daemon account, but you can use an account in the daemon group. The email is not used by PEAKS but is requested by the Mascot server.

Question: How do I configure Sequest for PEAKS inChorus?

Answer. It's not that difficult to do, just open up Edit -> Configuration -> Environment Preferences and go to the Search Engines tab. Once there, you just have to type in the location of various important parts of BioWorks. Click the Browse button next to each box to find them. They will automatically look for the default location. It's most important to find the sequest.exe, but it doesn't matter quite as much which .params file you choose as your default, because you'll likely be making changes to it. Furthermore, it doesn't matter much where you put the Sequest results by default.

Question: How do I install PEAKS on a computer running Windows Vista?

Answer. Download our easy to use Vista installation guide, specific to your needs.

Question: How do I install PEAKS on a computer without Internet access?

Answer. As you may have already discovered, after entering the registration key information into the designated window, you were presented with an error page. It requests that you go into the directory where the PEAKS files have been stored on your computer to retrieve a particular file (reg_log). Most users will have it stored in "C:\Program Files\PEAKS Studio 4.5\" on their computer. From here you will want to go into that folder and locate the "Ver" folder. This is the relevant folder for registration information. Since you have tried to enter the registration key information, a Registration Log file, called "reg_log", will exist in this directory. What you will need to do is copy that file onto either a floppy disk, CD, USB, or pass the file over an internal network to a computer with internet access. The file is very small so just about any transfer device will work. From a computer with internet access, you will need to log on to http://www.bioinformaticssolutions.com/OnLineRegistration.php and enter the relevant information into the boxes at the bottom of the page. When it says please load the "reg_log" file, you will do so by simply clicking on the Browse button, locating the "reg_log" file, and then pressing "Submit". This will both load the "reg_log" file into our system to validate the registration key and information provided and email you back a "license.lcs" file. You will need to transfer this file back to your offline computer (the one you wish to install PEAKS on to) and paste or place the file inside the "Ver" folder (C:\Program Files\Peaks Studio 4.5\ver). Then you are ready to load up PEAKS!