Wet lab protocols
Descriptive protocols for different types of wet-lab experiments. PDF versions of all protocols are available for download in the same directory where the protocol is found. For protocols with code blocks, the PDF version may have some of the code cut off for long lines, so I suggest you refer to the markdown version in these cases.
FOR ALL PROTOCOLS - refer to the health and safety guidelines of your own institute, as well as the MSDS documents for the described chemicals before use. Some of the chemicals and objects used are dangerous and should be handled with caution.
Quick links
- Related to proteomics
- Media preparation for SILAC
- Preparation of BSA chromatography and MS standard
- Preparation of a HeLa chromatography and MS standard
- In gel digestion for protein identification
- Preparation of immunoprecipitation samples for MS analysis
- SP3 protein clean-up
- TMT labeling of peptides
- TopTip desalting of peptides
- SlitPlate desalting of peptides
- Packing nanospray chromatography columns
- Total proteome analysis by mass spectrometry
- Related to Next Generation Sequencing
While these protocols have been validated to work in my hands, use at your own risk. If you have any issues or notice errors in anything that you find here, feel free to make a post in the wet lab protocols Issues and I will do my best to address it.
Dry lab protocols
Descriptive protocols for different types of dry-lab processes. The links below will send you directly to the RNotebook html version of the protocol. If you would like to download the R document to your own machine and follow along, simply open the RNotebook html by clicking the link, and click the ‘Download Rmd’ button in the top right corner. You can open this downloaded Rmd file in RStudio (or another text editor). If there is a supplemental text file associated with the protocol, it can usually be found on the actual GitHub page for that protocol.
In most of these protocols I use R, but sometimes I use Python. Usually, the Python code is used directly in the RNotebook using the reticulate package. In these instances, I do my best to detail my choice for one vs. the other, and what I am doing.
Quick links
While these protocols have been validated to work in my hands, use at your own risk. If you have any issues or notice errors in anything that you find here, feel free to make a post in the Issues and I will do my best to address it.