LC-MS
Here you'll find protocols and tips related to LC-MS analyses
Column preparation
Back to TopAt UWPR we use capillary columns, they are commercially available but can also easily be packed in your lab to save $$$
- LC-MS commonly used consumables (xls)
- Packing capillary columns (pdf)
- UWPR pressure cell
- Video: How to pull a capillary tip for LC/MS
- Video: How to pack a capillary column
- Video: How to Bomb-load Capillary Tips or Frits for LC/MS
- Video: Making Frits for LC/MS
- Making a fritted fused silica (pdf)
- FlashPack: Fast and simple preparation of ultra-high performance capillary columns for LC-MS. Kovalchuk SI, Jensen ON, Rogowska-Wrzesinska A. Mol Cell Proteomics. 2018 Oct 29. link
HPLC setup
Back to Topthe 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.
- LC-MS setup procedure EASYnLC(pdf)
- LC-MS setup procedure VanquishNeo(pdf)
- LC-MS setup procedure nanoAcquity (pdf)
- LC plumbing examples (pdf)
Mass spec related information and protocols
Back to Top- Avoid Contaminations (pdf)
- This file summarizes calibration solutions and calibration tips Calibrations (.xlsx)
- Simple peptide standards for LC-MS (xlsx)
- DIA overview page
- PRM overview page
- Skyline AngioNeuro_Orbitrap_PRM (zip)
- Skyline Promega 6x5_LCMS_Standard_Orbitrap_PRM (zip)
- Skyline Promega 6x5_LCMS_Standard_Hela_Orbitrap_PRM (zip)
- Skyline Sigma MSQC1_Orbitrap_PRM (zip)
- Skyline Hela_Orbitrap_PRM (zip)
- Skyline Pierce (7 x 5 Mix) (zip)
- Skyline Pierce (7 x 5 Mix)_Hela (zip)
- MRM/SRM overview page
- Skyline AngioNeuro_QQQ_SRM (zip)
- Skyline Promega 6x5_LCMS_Standard_Hela_QQQ_SRM (zip)
- Skyline for TSQ Altis method template "PRTC Hela" SRM (zip)
- Skyline for TSQ Altis method template "PRTC heavy" SRM (zip)
- Skyline Pierce (7 x 5 Mix) (zip)
- Skyline Pierce (7 x 5 Mix)_Hela (zip)
Hardware for LC-MS
Back to Top- UWPR nanospray ionization source
- Tips for upgrading to Win10 LTSC 2019 on TNG instruments (pdf)
- Tips for upgrading to Win10 LTSB 2016 on TNG instruments (pdf)
- Interfacing a Waters nanoAcquity with a Thermo mass spec (pdf)
- Fix for QEplus - nanoAcquity Contact Closure issues (pdf)
- Installing the nanoAcquity software with newer Xcalibur versions (pdf)
- Installing Xcalibur on Win 10 (pdf)
- Rebooting nanoAcquity after an error (with newer Xcalibur versions) (pdf)
- nano HPLC sparging kit parts list (xls)
- Guide how to setup alternate EASY-nLC solvent filters (pdf)
- LC plumbing examples (pdf)
- UWPR N2 switch for low flow applications (pdf)
- UWPR pressure cell
- Spark Holland injection needle (pdf)
- list of common materials needed for Thermo mass spec installations (xls)
- MS direct infusion line (pdf)
Miscellaneous
Back to Top- 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.