Proteomics services

Representative services

Protein identification
  • Protein gel band identification
  • Plasma/tissue – FASP or in-solution digest with stage-tip SCX and multiple fractions analyzed (typically 10)
  • Post-translational modification (PTM) identification – as above with enrichment of phosphopeptides, acetyl-lys, dimethyl-arg, etc.
Protein / proteomics quantification
  • Stable-isotope peptides and QQQ MS/MS-MRMs (Agilent Masshunter B.05; Skyline)
  • Label-free using Progenesis LCMS for aligning and comparing chromatograms)
  • Dimethyl labeling triplex stable isotope experiment with MaxQuant and Discoverer
Proteomics data analysis software
  • MaxQuant
  • Perseus
  • Proteome Discoverer
  • Mascot 2.4
Intact protein mass measurement, profiling, and quantification
  • Low-resolution ESI typically LC-MS
  • High-resolution ESI on FT-MS (Orbitrap, 7T LTQ-FT, 15T Bruker)
  • Extracted Ion Chromatogram (EIC) method (low or high resolution)
Reverse-phase LC-MS with fraction collection
  • LC-MS+ – Fractions reserved for top-down high-resolution FT-MS and other experiments
Top-down mass spectrometry
  • High-resolution ESI on FT-MS (Orbitrap, 7T LTQ-FT, 15T Bruker) with collisionally-activated or electron capture/transfer dissociation (CAD and ECD/ETD; Prosight PC 3.0)
  • Protein capture from complex fluids using immobilized antibody columns.
Native protein mass spectrometry
  • Static nanospray on Orbitrap/LTQFT to 4000 m/z
  • Nanospray or syringe pump infusion Bruker FTMS to 12,000 m/z

For protein or proteomics related inquiries, please contact Dr. Julian P. Whitelegge at or (310) 794-5156

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