LC-MS system

| LC(Liquid Chromatography) part

1. LC

2. HPLC

   • HPLC User Maintenance & Troubleshooting, Agilent
   • HPLC Columns
   • Nexera UHPLC/HPLC System, Shimadzu Corporation
   • Thermo Vanquish UHPLC FLEX [[]]
   • ACQUITY UPLCWaters

| MS(Mass spectrometry) part

1. Orbitrap based:

• Review article: Evolution of Orbitrap Mass Spectrometry Instrumentation [PDF | PMID: 26161972 | DOI Link]
  • Q Exactive-HF
  • Q Exactive-fusion
  • Orbitrap Exploris 240
  • Orbitrap Exploris 480
  • Lumos

2. Triple Quadrupole based

   • TSQ Quantum
   • TSQ Altis
   • SCIEX QTRAP5500
   • SCIEX QTRAP6500
   • SCIEX QTRAP7500

3. Protocol for metabolite extraction

   • From tissue/organ for HILIC LC-MS: PDF
   • From Plasma: PDF
   • From adherent cell line: PDF

Vendor companies

1. ThermoFisher
2. SCIEX
3. Agilent
4. Waters
5. Shimadzu Corporation

MALDI system

1. MALDI

   • Rapiflex, MALDI-TOF/TOF, Bruker
   • TimsTOF-Pro, Bruker: powered by the Trapped Ion Mobility Spectrometry(TIMS) [[]]
   • TimsTOF Pro 2, Bruker: powered by the latest Parallel Accumulation SErial Fragmentation (PASEF®) [Introduction video]

2. AP/MALDI

   • MassTech
   • TransMIT

Vendor companies

1. Bruker
2. MassTech™

Proteomics

• Bruker Proteomics solution
• Instrumentation
  • nanoElute (Bruker Daltonics)
  • 25cm * 75um * 1.6um C18 column(IonOpticks, Australia)
  • Column oven(Sonation)
  • captiveSpray Ion source(Bruker)
  • timsTOF Pro(Bruker Daltonics)
• Method
  • PASEF
  • dia-PASEF
  • prm-PASEF
• Data Processing
  • PEAKS Studio, PEAKS Online
  • MaxQuant
  • Skyline
  • ProteinMetrics

Ref. Labs

1. Lingjun Li Lab, University of Wisconsin Madison

2. West Coast Metabolomics Center, UC Davis

• Fiehn Laboratory for Untargeted Metabolomics
• Newman Laboratory for Lipid Mediators
• Hammock Laboratory for Inflammatory Metabolism

Metabolomics analysis softwares

1. MetaboAnalyst: v5.0
2. MZmine3
3. MS-DIAL
4. MaxQuant
5. SpatialMeta

Online courses

1. 2018 North American Mass Spectrometry Summer School(1st Annual)

   • MS-based compound identification in untargeted metabolomics, Oliver Fiehn, University of California-Davis
   • Protein Quantification by Mass Spectrometry Part II/Development and Application of Chemical Tags, Lingjun Li, University of Wisconsin-Madison

2. 2019 North American Mass Spectrometry Summer School(2nd Annual)

   • Ionization, Evan R. Williams
   • Quantitative Proteomics, Lingjun Li
   • Exploring Proteomes Using Discovery and Targeted Mass Spectrometry Approaches, Ulrike Kusebauch
   • Acquisition Methods-DDA, DIA and PRM, Jesse G. Meyer
   • Spectral Interpretation, Beatrix Ueberheide
   • Science Writing, Alicia Williams
   • Post-translational Modifications, Judit Villen
   • Mass Analyzers, Michael Westphall

3. 2021 North American Mass Spectrometry Summer School(3nd Annual)

   • Deconstructing a Mass Spectrometer, Mike Westphall/Kenny Lee
   • Separation Science of Complex Biological Mixtures, Susan Olesik
   • Tandem MS, Joshua Coon
   • Data Analysis and interpretation with MaxQuant and Perseus, Jürgen Cox
   • Publishing your Science, Shawnna Buttery
   • How to Set-up an LC Run, Laura Muehlbauer/Justin McKetney
   • How to Calibrate a Mass Spectrometer, Austin Salome/Trent Peters-Clarke
   • Post-translational Modifications, Evgenia Shishkova
   • Experimental Design for Quantitative Proteomics, Edward Huttlin
   • Metabolomics, Jessica Prenni
   • Lipidomics, John A. Bowden
   • Top-down and Native MS, Vicki Wysocki; nMS-to-SB
   • Data Acquisition Methods, Jesper Velgaard Olsen

4. 2022 North American Mass Spectrometry Summer School(4th Annual): Tutorial lecture topics include: Mass Analyzers, Ionization, Tandem MS, Chromatography, Shotgun Proteomics, Instrument Acquisition and Setup, Data analysis, and PTMs. Also planned are lectures workshops for scientific and professional development.

   • Exploring the “Social Network” within a Human Cell, Edward Huttlin
   • Future Technology Needs, Panel Discussion
     Panelists: John A. Bowden, Ben Garcia, Jessica Prenni, Edward Huttlin, Lingjun Li, Rachel Loo, David Geffen, Vicki Wysocki