Protocols

• Core Facility Protocols

  Protocols we use in the facility (updated May 2017)
  • Tissue and Cell lysis protocol
  • Protease Max In-Gel Digestion Protocol
  • In Solution Digestion Protocol
  • Using A SDS Page Gel to clean up an IP experiment
    Easy way to clean up an IP experiment
  • HyperSep Tip SPE
  • Digestion Proteins off Magnetic Beads
    You can use this to Digest proteins right off magnetic beads
  • Using Polyacrylamide to clean up a sample
    No need to even run a gel, watch out for Acrylamide modifications with this one!
  • SDS Page
  • Pulling and Packing your own nanospray columns
  • Using iRT retention time standards in Skyline

• Other Nice Protocols

  Protocols from other People that we find work well
  • Ingel Digestion Protocol 2
    This is another good ingel digestion protocol
  • Magnetic Bead IP and Digestion
    works great!
  • Immunoprecipitation protocols and Tips
    From Abcam
  • CONJUGATION OF MAGNETIC BEADS
    From the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry
  • Precipitation of Proteins
    Nice document comparing 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

• Duke Proteomics Core Facility
  They seem to have some really nice protocols here
• Coomassie Blue staining
  From Shared Proteomics
• Silver Staining
  From Shared Proteomics
• Destaining, reduction and alkylation
  From Shared Proteomics
• IMAC
  from Shared Proteomics
• Cell lysis (urea)
  From Shared Proteomics
• Cell lysis (ProteaseMAX)
  From Shared Proteomics
• 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
  Great protocol for Plant tissue
• Good Protein extraction and digestion protocol for HEK cells
  This is from Chris Collangelo @ Yale and was used with great success on the ABRF sPRG 2013 study
• Everything Dynabeads
• Protocols from UWPR

 Software Tutorials

• Maxquant Tutorial
• Perseus Tutorial (For Maxquant Data)
• MSconvert Tutorial