PEAKS Frequently Asked Questions
1. Question: What is .ANN format?
Answer: The ANN format is annotated data file in XML format. PEAKS uses it to save MS/MS information and peptide information. It supports both single MS/MS spectrum data and multiple spectra data. PEAKS accepts and saves file(s) in ANN format. ANN uses an ANN data file and an ANN index file (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. The directory has the same name as the ANN index file but with ‘dir’ as the extension instead of ‘ann’.
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. 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: 1024MB RAM, 1GB free space on hard drive.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. Question: How can I save the sequences resulting from auto de novo?
Answer: You can copy the predicted sequences by right clicking on the sequences, and select copy. This will copy the sequence of letter symbols to the clipboard. You may then paste them into a word processor or text editor. You can print images by clicking the right-most ‘Print result image’ button at the top of the main process window. Or you can save images by clicking the ‘Export results as image’ button. The printed or saved images look slightly different to those displayed on the screen.
9. Question: What is the difference between save data file and save all files?
Answer: Save data file: If current data file or the sequencing result of the selected data file(s) has been changed, PEAKS will save the data file and the sequence information in .ann format. Save all files: If there is more than one data file loaded, using "save all files" will save all the data files and their sequence information in their respective .ann format files. There is no need to select any files.
10. Question: We saw a green triangle on the m/z axis of the spectrum. What does that represent?
Answer: This green triangle is used to shown the location of the one charged precursor.
11. Question: Why I cannot delete a task from the Task Queue?
Answer: There are 2 steps to remove a task from the Task Queue: Disable the task running by clicking on “Enable task running” from the “Tools” menu to deselect it. Right-click the task in the Task Queue. From the popup menu, choose “remove”.
12. 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.
13. 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.
14. 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?
Answer: PEAKS will not run a database search if you select a single spectrum. This will not provide useful protein identification results. You must select the whole spectrum data file, then run auto de novo.
15. 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.
16. 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 150 to 250 spectra. We are working on scalability, but for now, try splitting your data up into chunks. Alternatively, it may be the result of a known bug in PEAKS 2.0. Please upgrade to PEAKS 2.1 or better. Yet another cause may be a Java conflict with windows NT. Upgrading to Windows 2000 or XP will solve the problem. If this is impossible, try reinstalling Peaks with a lower memory setting.
17. Question: I specify a tryptic digest, but the database search returns non tryptic peptides. Why?
Answer: PEAKS 2.0 does this to ensure that you are presented with peptides that resulted from extra cleavages. Later versions of Peaks have lifted this restriction to present the user with more flexibility. If you wish PEAKS 2.1 (or later) to find these, select "unknown enzyme".
18. 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.
