Chapter

Manual of Cardiovascular Proteomics

pp 227-245

Date:

Label-Free Quantification by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes

  • Sarah J. ParkerAffiliated withThe Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical Center Email author 
  • , Ronald J. HolewinskiAffiliated withThe Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical Center
  • , Irina TchernyshyovAffiliated withThe Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical Center
  • , Vidya VenkatramanAffiliated withThe Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical Center
  • , Laurie ParkerAffiliated withDepartment of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota
  • , Jennifer E. Van EykAffiliated withThe Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical CenterDepartment of Medicine, Johns Hopkins University School of Medicine

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Abstract

The large-scale identification and quantification of proteins by liquid chromatography mass spectrometry (LC MS) can be achieved by at least three general methods, categorized into targeted, data independent (DIA), and data dependent (DDA) acquisition modes. Each acquisition strategy has its own set of benefits and drawbacks, and the methods serve complementary purposes for the study of protein quantification in biological samples. While not specific to research in cardiovascular physiology, a long-standing but recently popularized proteomic approach, termed Data Independent Acquisition Mass Spectrometry (DIA-MS), promises unique strengths to complement and extend the existing capabilities of traditional “discovery” proteomic profiling by combining development of a peptide library and DIA-MS. In this chapter we will provide background on the DIA-MS technique, highlighting its fundamental differences relative to other mass spectrometry methods, and discuss important considerations for researchers interested in implementing this technique for their proteomic experiments.

Keywords

Data independent acquisition mass spectrometry Label-free Quantitation Peptide library Targeted analysis Untargeted analysis Proteomics