Boston University Biology

Proteomics Resource Page

This page contains the information requested by those who attended the April 24-25 training with Amersham Biosciences.

In order to view/print the pdf documents, you will need Adobe Acrobat Reader, which is free to download.

Reference Books and User Manuals:

2-D Electrophoresis Principles and Methods, 2nd Edition (newest). Download the pdf (1.1 MB)

2-D Electrophoresis Principles and Methods, 1st Edition. Download the pdf (672 K)

Dalt II Gel Apparatus User Manual. Download the pdf (624 K)

IPGphor User Manual. Download the pdf (568 K)

Dalt Precast Gel and Buffer Kit Manual. Download the pdf (2.2 MB)

Immobiline Drystrip Reswelling Tray Manual. Download the pdf (92K)

Calbiochem Detergents Booklet. Download the pdf (584K)

Fluorescence Imaging-Principles and Methods. Download the pdf (15.5 MB)

To make the Amersham Plus-One silver stain kit (17-1150-01) Mass Spec compatible, download the protocol: pdf (4K)



Insert the following step after step 6 in either procedure A or B:  Add 40 µl Co-precipitant on top of the pellet (for larger sample size, add a volume of Co-precipitant that is 3-4x the size of the pellet.)  Carefully reposition the tube in the centrifuge as before (i.e., cap-hinge facing outward).  Centrifuge the tube again for 5 minutes.  Use a pipet tip to remove and discard the Co-precipitant.

Miscellaneous Q & A From the Sessions:

In this section, the answers are either placed in the body of this page, or, where applicable, a link to download a file (usually a pdf) is provided.

PPA-Piperidino propionamide-In the Ettan gel buffer Tris is replaced by PPA which allows a pH below 7. Thus the gel matrix can not hydrolyze during storage.

Here is a link to an article showing how the laemli buffer system migration compares to that of the PPA buffer system in the Ettan PreCast gels

Ruby versus Cy 2,3,5 crosstalk question:

The excitation and emission filters are distinct for all the dyes and Sypro ruby. The major problem is that Sypro ruby fluoresces across such a wide range (excite around 400, emission around 630) that you will get some Sypro ruby signal if you were to try to re-image the Cy dyes. This means that once you've stained with Sypro ruby, you can no longer go back and re-acquire a Cy dye image, since the quantitation would no longer be correct. So there is cross-talk in the Cy dye channels due to signal coming from Sypro ruby.

Protocol-manual digestion methods for gel plugs. Download the pdf (20K).

For low salt digestion, use 7-20mM ammonium bicarbonate/50% methanol instead of 50mM ammonium bicarbonate/50% methanol solution.

Cy Dye bound to the peptides and measurement with Mass Spec:

The bottom line is that due to the very low abundance of the Cy Dye to be potentially bound to the protein that it is not an issue in detection with the minimal labeling (to the lysine residues) (the saturation labeling through the cysteine residue is mass spec. compatible and needs the Cy Dye MWt to be added into the data base search for being bound to the cysteine residues)

Immobilized pH gradients-table of gradients. Download the pdf (1 MB)

Sypro Ruby staining protocol of 2D gels. Download the pdf (68K)

Duracryl (to cast firmer polyacrylamide gels) can be purchased from Genomic Solutions

The reversible stain for storing IPG strips at room temp. Download the pdf (12K)

The video camera we used for the training presentation is from:

FlexCam Pro 3.1:
Source: Videolabs, Inc., 10925 Bren Road East, Minneapolis, Minnesota
55343, (612)988-0055, Fax (612) 988-0066

Bind-silane method for gelbond-backing gels. Download the pdf (8K)

Reference describing the method to make new Sypro Ruby stain. Pubmed Reference.

Reference for running IEF of proteins with basic pI. Pubmed Reference

Basic pH gradient with high sample loads. Pubmed Reference. Brief method pdf (4K)

Reference describing increase in [DTT] to 3% to improve basic pI resolution. Pubmed Reference.

Acid violet staining of immmobiline gels and strips: Patesotos et al. (1988) Electrophoresis 9:488-496. Download the pdf of the protocol (4K).

The use of glycerol and isopropanol in the rehydration buffer and discussion of electroendosmosis. Download the pdf (4K)

Test sample protocols-trial preps that almost always work well for 2DE:

Carrot Seed (this is the one we did in the class) (pdf 16K)

E. coli (pdf 4K)

The use of IPG strip with hydrophobic proteins. Pubmed Reference.

Capacity of polyacrylamide gels. Pubmed Reference.

Diffusion Blot protocol-western method used for backed gels-gels can then be further processed (Spot picker, etc.). Download the pdf (4K).

Spot-picker parameters for unbacked gels. Download the pdf (4K).

The Tris tricine buffer system for the DALT 12. Download the pdf (4K)

Molecular Wt. versus gel percentage - Look at page 635 of the Amersham 2002 catalog-the table is at the bottom

The kits for membrane bound protein extraction etc is here:

Cell Wash for cultured cells prior to harvesting for IEF:

Salt carry-over from growth medium or wash solution can be significant. Salt-free buffer/osmoticum should be used for washing (10 mM Tris / 250 mM sucrose pH 7.0)


Protein Science Resources on the Web:

Angelika Gorgs website for her 2D manual (describes IPG gel pouring) - also stuff on running basic strips and animal tissue preparation (brain etc):


Swissprot can be accessed through the ExPasy website:

Amersham discussion zone is here and the 2D discussion zone is under the Biotechnology section:

people have visited this page since May 8, 2002