Could anyone explain to me some basics on protein research protocols?

Sorry to hear that you do not have a great mentor. A good mentor should tell you these things, and never leave you helpless.

One thing that confused me when I started to work in molecular labs, is that everyone seemed to have a different protocol. That was very confusing, until I realized that maybe certain conditions/buffers were more important than others. Or, in other words, I started to see that all these protocols actually had some things in common. Maybe the concentration of a component differed, or the time, but there were also common themes. I figured that these might be key components to a protocol.
I also learned that every lab and even every person within a lab might use a different protocol. If you transfer a working protocol from lab A to lab B, it might not work at all! That is frustrating, but the best thing is to apply the protocol that works in a certain lab.

I wish I could answer some of your specific questions.

Here are some websites that might answer some of your basic questions.
http://www.ruf.rice.edu/~bioslabs/studies/sds-page/gellab2.html#gelprep  (has some background info)
http://www.encorbio.com/protocols/SDS-PAGE.htm
http://mach7.bluehill.com/proteinc/tutorial/sdspage.html  (has some basic recipes)

I hope you can find a nice person in the lab to help you with more practical questions. But even if you do not like this lab, you will still learn a lot, and you will be able to use that knowledge in your next job or internship. I did not like my first lab either, nor did I have a great mentor, but I loved my second rotation and stayed there to do my PhD!

You need to match the technique to the questions you are asking.

Here are a few Protein techniques:

Western: (SDS-PAGE) This technique uses gels to separate proteins loaded into a gel. Usually the protein pattern is "transferred" to a membrane that facilitates subsequent analysis. You can then identify specific proteins using antibodies, and quantify the amounts of each protein. You can tell if a protein was phosphorylated or dephosphorylated, has increased or decreased amounts, etc.  You would usually use this technique to examine the effects of your treatment (drug, overexpression, temp, whatever) on specific proteins. See links posted by Bioliz.

Florescence: A very important tool. There are many techniques using Fl., like Microscopy, Cytometery (FACS), Florescent in-situ hybridization (FISH). Basically, it allows the visualization of a protein, DNA, RNA or even entire organelles (from the entire nucleus to mitochondria). Then you can quantify, qualify, sort, calculate kinetics, look at spacial placement, structure and more.

Molecular biology: You are familiar with this field, but protein labs use these tools also, to overexpress proteins, knock down proteins and create all sorts of constructs.

Immunoprecipitation: This is used to find a physical connection and affinity  between proteins. Be aware that currently you need to plan very good controls for this type of experiment, many reviewers do not like it so much. This frequently is a pre-step to SDS-PAGE.


You need to shadow someone. Just ask one of the post-docs and PhD students in the lab to join them, if your instructor does not assign you.
You need to ask your question first. Once you have your hypotheses and question you want to answer, either ask here again what technique is appropriate, or ask someone in the lab what technique is appropriate.
Good luck