KingFisher Apex

Semi-automated processing of samples:

• Sample clean-up and digestion via SP3 workflow (Hughes et al., 2019, PMID: 30464214)
• Fe-IMAC enrichment of phosphorylated peptides (Leutert et al., 2019, PMID: 31885202)

Agilent 1260 Infinity HPLC

• Offline fractionation of peptides by high pH reverse phase chromatography
• Offline fractionation of crosslinked peptides by peptide size-exclusion chromatography

Ultimate 3000 HPLC

• Offline fractionation of peptides
• Online C18 reverse phase chromatography directly coupled to the mass spectrometer

Vanquish Neo HPLC

• Online fractionation of peptides with C18 reverse phase chromatography directly coupled to the mass spectrometer

Q Exactive Plus

High-resolution mass spectrometer

• Equipped with advanced quadrupole technology and high-resolution Orbitrap
• Fragmentation of precursor ions using HCD
• For analyses of peptides in DDA and DIA mode

Orbitrap Lumos Tribrid

High-resolution mass spectrometer

• Equipped with advanced quadrupole technology, a high-resolution Orbitrap and synchronous precursor selection (SPS)-able Iontrap for MS3-based methods
• Fragmentation of precursor ions using HCD, CID or ETD
• For analyses of peptides in DDA and DIA mode including MS3-based methods and ETD fragmentation for PTM analysis

Orbitrap Exploris 480

High-resolution mass spectrometer

• Equipped with advanced quadrupole technology and high-resolution Orbitrap
• Fragmentation of precursor ions with HCD
• For analyses of peptides in DDA and DIA mode, especially well suited for DIA due to faster transit times

Orbitrap Astral

Next-generation, high resolution mass spectrometer

• Equipped with advanced quadrupole technology, high-resolution Orbitrap and the new, sensitive, fast and high-resolution Astral analyser
• Fragmentation of precursor ions with HCD
• For ultra-deep, sensitive analyses of peptides in DDA and especially DIA mode

DDA data

• MSFragger/FragPipe
• MaxQuant
• Skyline
• R for statistical analysis and data visualization

DIA data

• DIA-NN
• Skyline
• R for statistical analysis and data visualization

Crosslinking data

• pLink3
• xiView