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.
Always try to use the most recent versions of protocols to get the most up-to-date pipelines. For example, the 'Dual whole transcriptome and proteome analysis' protocol includes the most up-to-date versions of the lysis, SP3, and peptide clean-up protocols, but the individual ones may not be quite up-to-date. Use the last updated date as a guide. I try to update the individual ones, but I don't always have time to keep them up to date.
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.
- 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
- Dual whole transcriptome and proteome analysis
- FFPE tissue proteome analysis
- Extracellular vesicle proteome analysis
- Related to Next Generation Sequencing
- Troubleshooting
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.