Here you'll find protocols and tips related to LC-MS analyses

Column preparation
for LC-MS we use capillary columns, they are commercially available but can also easily be packed in your lab to save $$$

HPLC setup
the following documents are guidelines to setup the capillary trap/column on our LC-MS systems, this is intended as a supplement to the hands on training required to use the UWPR instruments.

Mass spec related protocols
maintenance,calibrations, etc

Hardware for LC-MS


  • Common Mass Spec Background Ions go to page
  • Mass Spec Background Ions: Repeating Units go to page
  • UCSF Prospector Trypsin Autolysis Products go to page
  • UWPR_CommonMassSpecContaminants spreadsheet xls
  • Mass Spectrometry Software: ESIprot 1.0
    ESIprot 1.0 is a nice tool which enables the charge state determination and molecular weight calculation of proteins
  • Venny
    A nice and easy tool to crate Venn diagrams.
  • BoxPlotR
    BoxPlotR: a web-tool for generation of box plots.