Instructions for online pf2d submissions

PLEASE NOTE: Due to continuing concerns posed by potential bioterrorism agents (select agents), our online submission form requires that you provide us with information on the original biological source of any DNA from which you will be asking us to obtain sequence. "Original biological source" refers to the organism from which the DNA was first found in nature (human, HIV, Staphylococcus aureus, etc.). If you simply put a nonspecific term such as "E. coli clone", this will not be sufficient. We realize that adding yet another field to fill out on these forms can be tiresome, but this information is necessary to protect our staff against potential legal difficulties. Thank you very much for your understanding.

            - David W. Dyer, Ph.D.

 

 PF2D Submissions

1. Please submit samples in a lyophilized form. If you are submitting tissue samples, please homogenize (or similarly process) the tissue and then lyophilize for submission. Submissions of cell cultures can be pelleted and dried. Samples should not contain detergent, as the micelle concentration of the detergents that we use will be affected, causing shifts in migration. If your sample needs to be lysed, we will do that using Beckman's protocols.

2. You will need to do a protein assay on your sample before submission to ensure that we are working with the proper amounts. To assess protein concentration, we suggest using Pierce's Micro BCA Protein Assay kit (Product# 23235). The maximum amount that can be loaded onto the machine is 5mg. We prefer to run ~2mg, but can go much lower depending on what is needed for a particular sample. If the amount of sample is a problem, please contact us before submitting this sample, so that we can discuss alternatives. Once a sample has been submitted to us and prepped for a run, the sample cannot be used past that date of preparation. So, if too little protein is in the sample, we cannot save it for future use due to the effects of the preparation buffer within that we use for the first dimension separation.

If you are submitting multiple samples for comparison to one another, it is important that they are processed in the same way, and are at the same final protein concentrations, for accurate comparisons.

3. Once you've submitted a sample, we will send you an email letting you know the approximate date that your sample will be run. Each sample takes one week to run in order to get information from both the 1st and 2nd dimensions. Obviously, since a full two-dimensional separation takes a long time, scheduling for this is critical, for the sake of efficiency. So, we ask that your sample be submitted on a Thursday in order for it to be run by the following Monday, if that week is available. If you require only one dimension to be run, then we will try to fit this run in as soon as possible.

4. After your separation is complete, we will send you an email with your data (the ability for you to access your data from our website is in development). Below is a list of what types of data you will receive. At this time, your 96-well blocks of collected samples will be ready for pick-up. There will be one block for the 1st dimension collection and multiple blocks for the 2nd dimension (~20 blocks). The blocks are and should be stored at -80°C. You will need to pick up your blocks of resolved proteins within 3 weeks of the run time, since our -80°C freezer space is limited.

5. Pricing for one sample to run through both dimensions is $700. For pricing of specialty runs, please see our Fee Structure page.

6. An SUR# (OUHSC) or PO# (off-campus) must be given at the time of submission.
   
   Shipping Address:
   
   The Laboratory for Genomics and Bioinformatics OUHSC
   Attn: Jenny Gipson
   975 NE 10th Street, BRC1106
   Oklahoma City, OK 73104
   

7. An on-line submission form must be filled out completely.

8. If you have any additional needs or questions, please contact Jenny Gipson (405-271-2337) or Dr. Allison Gillaspy (405-271-1201 ext. 2).

   
   

 SUBMISSION FORM

             pf2d online submission form

PF2D Data Output

To view your data, you will need to download the PF2D Software and its video tutorial from our website. Please take the time to go through the video tutorial, as this will make your life (and ours!) easier when you start to analyze your data using the PF2D software.

Each sample run through the 1st and 2nd dimension of the PF2D will have 5 sets of data:

1. .pdf files - for easy viewing of the data
2. .dat files - These files can only be opened with the 32Karat software that comes with the PF2D. The .pdf files will have everything you need, but we give you these files in case you need to refer back to them.
3. .vue file - We will import your .asc files into ProteoVue in order to create this file to be used in DeltaVue
4. .asc files - for importing into ProteoVue, then creating a file for DeltaVue (in case you decide to change your pH parameters, or change samples in a file, etc.)
5. Excel file - This file shows where each 2nd dimension fraction can be located in the blocks. The "Block Display" (front page) is an overall view of the blocks. The first number represents the 1st dimension fraction number of the sample, while the second number indicates the further fractionation steps of that original fraction. The "Fraction Listing" (2nd page) shows each fractionation along with the time it came off the column. This will help you locate the exact well for a particular peak.
6. .f1d file - This is a file created by the newest version of the PF2D software. It can be used with the new Vizualize analysis software which picks the peaks for you and allows for multiple sample comparisons. We are unable to provide this software on our website, but we do have it available on an extra computer in our lab for customer use.