Frequently Asked Questions:
1. Q: Is PPS 1.0 a predictor for post-translational modification (PTM) sites prediction?
A: Principally, not. We desinged PPS 1.0 as a fast and convenient sotware to scan known or highly conserved/identical PTM sites in given proteins. And such an analysis will be helpful for experimentalists to avoid duplicated studies. Also, although the prediction ability of PPS is limited, we still found ten thousands of highly potential PTM sites in eukaryotes. We recommend that you can use PPS 1.0 firstly to scan known or highly potential PTM sites in your proteins, then use special predictors (eg., GPS 2.0) to predict potentially novel PTM sites.
2. Q: How to use PPS 1.0 software?
A: You can find the latest version of PPS at http://pps.biocuckoo.org/down.php. Then download and install the PPS 1.0 software to your computer. Currently, PPS 1.0 is implemented in JAVA and could be installed on a computer with Windows/Linux/Unix/Mac OS. And we also wrote a manual for users which included in the installation package. Also, you can use the online service of PPS directly by clicking on ">> Go to PPS 1.0 Online Server". Then please input your one or multiple protein sequences in FASTA format into INPUT form. Then please choose PTM type, and click submit to start searching.
3. Q: I have 20,000 proteins for prediction, what should I do?
A: For a large-scale prediction, we recommend two approaches for you. You can input the sequences for 20 times, with 1,000 proteins per time. Also, please download a stand-alone software of PPS 1.0 linked as below. In the stand-alone versions, the limitation of sequences number is removed. You can use "Batch Predictor" in the local software for a large-scale prediction.
4. Q: I can't open the software properly, what should I do?
A: We have tested PPS 1.0 on several internet browsers, including Internet Explorer 6.0, Netscape Browser 8.1.3 and Firefox 2 under Windows XP Operating System (OS), Mozilla Firefox 1.5 of Fedora Core 6 OS (Linux), and Safari 3.0 of Apple Mac OS X 10.4 (Tiger) and 10.5 (Leopard). For Windows and Linux systems, a latest version of Java Runtime Environment (JRE) package (JAVA 1.4.2 or later versions) of Sun Microsystems should be pre-installed for using the PPS 1.0 program. To get the latest version of the JRE, please visit the http://java.com page, and choose the proper JRE package based on your operating system and browser. For convenience, you can also download the JRE packages from our website. However, for Mac OS, the PPS 1.0 could be used directly without any additional packages. Finally, if you can still not view the program properly, please send use an email and tell me the OS information on your computer. We will resolve the problem ASAP.
5. Q: I have a few questions which are not listed above, how can I contact the authors of PPS 1.0?
6. Q: I was trying to install the software in Mac OS but my installer says the file is damaged. How can I properly install the software in Mac OS?
A: By default, Mac OS 10.8 or later only allows users to install applications from 'verified sources'. In effect, this means that users are unable to install most applications downloaded from the internet. You can follow the directions below to prevent this error message from appearing.
(1) Open the Preferences. This can be done by either clicking on the System Preferences icon in the Dock or by going to Apple Menu > System Preferences.
(2) Open the Security & Privacy pane by clicking Security & Privacy.
(3) Make sure that the General section of the the Security & Privacy pane is selected. Click the icon labeled Click the lock to prevent further changes.
(4) Enter your username and password into the prompt that appears and click Unlock.
(5) Under the section labeled Allow applications downloaded from, select Anywhere. On the prompt that appears, click Allow From Anywhere.
(6) Exit System Preferences by clicking the red button in the upper left of the window. You should now be able to install applications downloaded from the internet.
An application of PPS 1.0:
proteome-wide study of creation or disruption of PTM sites
by alternative splicing
As an application of PPS 1.0, we used PPS 1.0 with PMP(7, 7) to scan 13 064 alternative isoforms and their 6 900 major isofoms in H. sapiens, separately. Totally, we computationally identified 1 168 and 125 PTM sites specifically existed in 438 major and 87 alternative isoforms, respectively. And the detailed results are available: Sup_table.xls