title: MARQUIS: a multiplex method for absolute quantification of peptides and posttranslational modifications.
abstract: Absolute quantification of protein expression and posttranslational modifications by mass spectrometry has been challenging due to a variety of factors, including the potentially large dynamic range of phosphorylation response. To address these issues, we have developed MARQUIS-Multiplex Absolute Regressed Quantification with Internal Standards-a novel mass spectrometry-based approach using a combination of isobaric tags and heavy-labelled standard peptides, to construct internal standard curves for peptides derived from key nodes in signal transduction networks. We applied MARQUIS to quantify phosphorylation dynamics within the EGFR network at multiple time points following stimulation with several ligands, enabling a quantitative comparison of EGFR phosphorylation sites and demonstrating that receptor phosphorylation is qualitatively similar but quantitatively distinct for each EGFR ligand tested. MARQUIS was also applied to quantify the effect of EGFR kinase inhibition on glioblastoma patient-derived xenografts. MARQUIS is a versatile method, broadly applicable and extendable to multiple mass spectrometric platforms.
authors.affiliation: 1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Curran
authors.affiliation: Thermo-Fisher Scientific, San Jose, California 95134, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Radiation Oncology, Mayo Clinic, 200 First Street South West, Rochester, Minnesota 55905, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Ma
authors.affiliation: Department of Radiation Oncology, Mayo Clinic, 200 First Street South West, Rochester, Minnesota 55905, USA.
authors.forename: Jann N
authors.initials: JN
authors.lastname: Sarkaria
authors.affiliation: 1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Forest M
authors.initials: FM
authors.lastname: White
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D066246:ErbB Receptors / Q000378:metabolism; D005909:Glioblastoma / Q000378:metabolism; D006801:Humans; D008024:Ligands; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D009368:Neoplasm Transplantation; D010455:Peptides / Q000737:chemistry*; D010766:Phosphorylation; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D014443:Tyrosine / Q000737:chemistry
chemical_list: D008024:Ligands; D010455:Peptides; D014443:Tyrosine; D066246:ErbB Receptors