Protocols we use in the facility (updated Sept 2023)
- Tissue and Cell lysis protocol
- Protease Max In-Gel Digestion Protocol
- In Solution Digestion Protocol (Urea In-Solution)
- Digestion Proteins off Magnetic Beads
- Pulling and Packing your own nanospray columns
- Using iRT retention time standards in Skyline
Other Nice Protocols
- Using Polyacrylamide to clean up a sample (no need to run gel; search with Acrylamide modifications)
- SDS Page
- Using A SDS Page Gel to clean up an IP experiment
- HyperSep Tip SPE
- Ingel Digestion Protocol 2
- Magnetic Bead IP and Digestion
- Immunoprecipitation protocols and Tips (From Abcam)
- CONJUGATION OF MAGNETIC BEADS (From the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry)
- Precipitation of Proteins (compares various protein precipitation methods)
- Metabolite extraction prior to proteomics
- Plant Protein Extraction that usually works
- Good Affinity Purification Nature Protocols paper
Protocols from Other sources
I have not tried all of these. Let me know if they work for you.
- Duke Proteomics Core Facility
They seem to have some really nice protocols here - Preparation of HeLa peptides for LC-MS (From Protocol Exchange)
- Peptide Fractionation and Clean-up Protocols (From the UWPR Proteomics Resource Center)
- A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis(Plant tissue)
- Good Protein extraction and digestion protocol for HEK cells (Chris Collangelo @ Yale and was used with great success on the ABRF sPRG 2013 study)
- Everything Dynabeads
- Protocols from UWPR
