1. Introduction

Protbase is the new integrated system developed by the Bioinformatics Core Facility for providing storage, dissemination and analysis of experimental data from the Proteomics Core Facility . From a centralized login screen PFC users can submit service request, follow up the results and view/download all the details of their current and past experiments.

This system will umbrella
(1) on-line sample submission,
(2) sample tracking,
(3) billing,
(4) sample work-up (protocols),
(5) experiment progress,
(6) proteomic outputs (Sequest, DtaSelect, Contrast, annotated 1D and 2D gel images),
(7) other informatics support per proteins identified.

This resource will be undergoing development and many new features will be added as we go along. In future users should be able to compare results from multiple experiments and obtain integrated genome and proteome information for proteins of interest.

 

1.2. User Profiles

The site can be only be accessed by a User id and password that has been provided by the facility core OR by creating a New Profile in the System.

If you have already used the Proteomics Facility Core in the past then a password has been mailed to you at your given email address. You can access this site by using your email id as the user id and the password sent to you by email.

If you have forgotten your password click the forgotten password button, put in your email address and your password will be emailed to you.

If you are a NEW USER then CREATE a profile. Completely fill up the following form. Subsequently you can submit/view experiment details by logging in.

If you are an Existing User you can change your password / Edit your profile once you login see 1.3.1

1.3. Home Page Menus



Following menus are available to navigate thru the home page navigation bar.
1 This is the main login page to the online system
2 This is the Documentation/Help for the online system -Protbase.
3 Sample Submission form “ This form has to be completed online before bringing the sample to the PFC. Please read further in Section 1.3.2
4 This takes the user to a page that can access all the stored details of the submitted experiments. Read more in 1.3.3.
5 If you are an existing user you can edit your profile using this button. Please read further in Section 1.3.1.
6 This will log out the user. Make sure you logout of the system once your work is done.
7 This is a link to the BioResource for Array Genes website at www.biorag.org.
8 About Protbase Development and production details.
1.3.1. Edit Profiles

Please make sure to Update your profile first time while logging into the system (if an old user) and in future if there are any changes to email, phone no. etc.



1.3.1.1. My PIs

This will take you to the list of your current PIs and Old PIs. You can use the Edit Profile form to change your PI anytime. All the PIs get added to the list. This option is provided since researchers might change their PI at anytime. A change PI option is also provided in Submit Service Request Menu for convenience of changing PI while submitting a new experiment and getting the profile updated automatically. Read more in 1.3.2.4.



1.3.2. Submit Service Request

To request service from Proteomics Facility Core users will have to logon to this integrated system and submit the details of the samples and goal of the experiment.

Once you Complete this form and submit, you will have to take a PRINT OUT of submitted request details and take it along with the samples to the Facility.


Once you submit the request, this page comes up Print it out and take it to The Proteomics Facility Core with the Samples.



1.3.2.1. Experiment No.

This is a six digit Experiment No. that is provided by PFC on sample submission. This number will be automatically assigned to the Users Service Request by the Protbase. This Experiment Number is the ID for tracking the samples, sample processing, results of the experiments etc. All the features provided by this online system to view the complete details of an experiment can be accessed by this Experiment Reference No. If you loose this number for any of the Experiments, log into the system and it will bring up list of all the Service Requests you have made at PFC by their Experiment Number.



Other Navigational buttons:

1.3.2.2.1.3.2.3.1.3.2.4.


1.3.2.2. Edit Submitted Request

You can Edit a Service Request ONLY before the samples are brought over to the Lab. Once the samples are handed over and process entry has been made by PFC NO Editing can be done on that request.

Users can Enter an Experiment Number assigned upon Sample submission, this will bring up the Submission details and changes can be made accordingly.



1.3.2.3. View Submitted Request

Entering an Experiment No will bring up the Sample submission Summary. Click on the Sample details button and the page will display all the data entered for all the samples for that Service Request.



1.3.2.4. Change PIs

If a Researcher who has been a user of PFC earlier and is now working with some other PI than the one he has been working before, use this option to change the PI. This change will update the User Profile to reflect the current PI.

When you change your PI from that time onwards all your new experiments will be associated with the new PI you opted and can be viewed by him/her. Your old experiments cannot be viewed by your new PI. Your new experiments cannot be viewed by your old PI. If you want either them to view any experiments which they cannot because of these restrictions, you will have to make those experiments shared (See 1.3.4.)

The My PIs button will take you to the list of current PI and Old PIs.



1.3.3. View/Download Experiments

***We have incorporated experiments from January 2004 to July 2004 for all the Existing Users of PFC. But users might not find all the details and also the output results might not have been integrated properly because the information for the existing experiments had not been stored in a proper manner and had to be compiled from different sources.



1.3.3.1. Entry Page

This takes to the Page that lists all the experiments and their Progress Status submitted by the Researcher. All the Experiments for a User are identified by the six digits Experiment Numbers assigned by the System. This will be the main page to go to More Details for any experiment.



1.3.3.1.a. For User

For USERS who submit experiments (students/Postdocs/researchers) the following page is displayed.

This will show the Experiment Progress and upon completion will provide links to the results of the Experiments. See Section 1.3.3.3. for this Column



1.3.3.1.b. For PIs

Principal Investigators can View Experiments of all the researchers of their lab.
In addition they can Search By:

1) Experiment Reference No.
2) By Date



1.3.3.2. Submission details

The Online Sample submission Details Can be accessed from Here



1.3.3.3. Output Column

This column shows the Progress of the Experiments at PFC and Links to Results upon Completion



1.3.3.3.a Status of the Experiments

1) Upon online Submission for that Request Status shows up as waiting for samples at PFC. This will change once the samples are handed over to the PFC and the staff has made entry for the Sample Process

2) Once the Sample process entry has been made by the PFC staff, it will show Experiments in progress results pending.

3) When the results of the Experiments are in, if they are Outputs like Gels and Sequest results for MS/MS expts there will be links for the user to view the results. As soon as ANY one of the above results is uploaded to the servers, a link to view result will be available and an Email will be send to the User to View their results. Subsequently whatever results follow users will receive emails for all of them.

4) If there is none of the above output for the request submitted eg. the request is just the Confirmation of molecular weight etc., the output column will say PFC will contact you on completion. You will have to get the results in these case from PFC. This is temporarily and we are working to integrate chromatogram and spectra results from MALDI etc. Once these are available as download, such results will also be available through web interface too.

5) Notes from PFC staff can be viewed from the Notes link.

For all the detail information and explanation about the results contact the PFC personnel.



1.1.3.3.4. Sequest Results

The Sequest link in the Output column will take to the Sequest browser. The drop down menu will show all the samples for which MS/MS spectra analysis is available. Select a sample and click Run, this will take to the Sequest Summary Page.

The Result files in the drop down menu are named based on the Naming convention displayed via a link on the page.







We are working to include more ways of passing over the interesting peptides from the Sequest Summary pages to other analysis software.


1.3.3.4.a. DTA Select

DTA Select provides the means of filtering Sequest summary file for the best results based on certain parameters. This is still under development. We are working on the HTML and the text Output, in order to organize it better for viewing and interpretation of results.

An online form would appear with sequest results to get a summarized output from DTA Select.




1.3.3.4.b. DTA Contrast

Soon we will be adding the DTA Contrast Feature which will take spectra results from multiple samples and Compare and Contrast for similar and differential peptides amongst Samples.

An online form would appear with sequest results to get a summarized output from DTA Select.



1.3.3.4.c. SALSA

Similar to Sequest we will be providing access to SALSA results in future for users interested in specific analysis of Peptides.



1.3.3.4.d. Integrating Sequest results with Genome and Proteome Information.

We are working on a Feature where from Sequest Summary pages, DTA Select and Contrast peptides can be selected for detailed genome and proteome information from the Bioresource of Array Genes at www.biorag.org. There will also be an effort in future to integrate results from samples on which both gene expression and proteomics studies have been done.



1.3.3.5. Gel Results and Details

Clicking on 1D and 2D links in the Output Column will bring up Images of the gels run for that Experiment.

***For the Experiments that have been done before July 2004, Gels have been integrated with Experiment IDs into the database. Although these have been entered without proper sample information and other details. This is because relationship between gel images, samples and other details were not recorded properly within an experiment.

For the new experiments the Gel images are displayed Sample wise.

The links to the Gel Experiment Details lists the Gel protocols, The Staining Protocols and other details about the Gel Run. Images with Band or Spot annotation are available as JPEG but a high quality original TIF image can be Downloaded.

Detailed information about Bands/Spots identified in the Gel will be available in future. Molecular weights will be shown for Bands from 1D gel. PI ranges and molecular weights will be shown for spots from 2D gels. Once the Gel processing software in PFC is configured properly for Spot Picking, Volume/Intensity of Spots will also be available for making comparisons between the gels.

There will be a feature in future to add annotations to the Spots by the Users after their experiments and results analysis.



1.3.4. Share Experiments

If a user wants to share an experiment with any other researcher, he/she can make their experiments shareable using this feature.

The only condition is that the other researcher has to be a user of Protbase, in other words his/her User Profile should exist in the system. If necessary a new profile can be created by the person with whom the user wishes to share the experiments.



Menu options for sharing:
1.3.4.1.1.3.4.2.1.3.4.3.1.3.4.4.


1.3.4.1. Share Experiment

Enter the Experiment Number and enter the Last Name of the person with whom the experiment is to be shared.

If there are people with this name in the system, it will come up with the email IDs and Complete Name of all of them.

If the Names donĖt match to the Person you are looking for Or there are No names found in the System, you need to request the other Researcher to create a Profile. For this you need to put in his complete email ID as shown below. An email will go to that person to create a profile.

After the shared request is submitted an email will go to the user to confirm that he/she has requested to share the XY Experiment with XY Researcher. Once the confirmation is received by the System, the researcher will be sent an email to view the shared Experiments.



1.3.4.2. My Shared Experiments

This will take the user to all their Experiments that they are sharing with other researchers.



1.3.4.3. Remove Share

A User can remove shared experiments whenever they wish by entering the Experiment No. and the shared will be Disabled.



1.3.4.4. Shared from Others

This is the list of the Experiments from Other Researchers that the User is sharing.



1.3.5. Logout

This will log out the user. Make sure to log out after every session. This is especially for people using public computers or shared computer systems.



1.4. Frequently asked Questions

******Yet to come********





For any questions regarding Protbase or Bioinformatics Core contact Dr. Ritu Pandey

For any questions regarding Proteomics Facility Core Service contact Dr George Tsaprailis

Protbase is developed and maintained by the Bioinformatics group at Southwest Environmental Health Sciences Center & Arizona Cancer Center.© 2003-2006 University of Arizona. All Rights Reserved.