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How hybrid mass spectrometers with multiple analyzers and dissociation methods will transform protein sequence analysis
Author(s) -
Coon Joshua J.
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.306.3
Subject(s) - orbitrap , mass spectrometry , tandem mass spectrometry , stable isotope labeling by amino acids in cell culture , chemistry , tandem mass tag , proteome , isobaric labeling , proteomics , quantitative proteomics , characterization (materials science) , dissociation (chemistry) , computational biology , chromatography , protein mass spectrometry , biological system , analytical chemistry (journal) , nanotechnology , biochemistry , biology , materials science , gene
We describe the use of new mass spectrometry technology for the large‐scale characterization and quantification of proteomes. The new instrument allows for the implementation of multiple peptide dissociation methods and for the automated selection of each in a real‐time based on multiple precursor attributes. Protein quantification is readily accomplished through use of isotopic labels – either SILAC or iTRAQ. The instrument will propel top‐down proteomics by combining ETD and Orbitrap detection to achieve direct analysis of intact proteins on a sub‐second timescale with ~ 300 ppb mass accuracies. Such mass accuracies are used to directly annotate tandem mass spectral peaks with ion type and chemical composition. We demonstrate these and other aspects of the instrument on a variety of applications involving human embryonic stem (hES) cells. In particular we identified over 8,000 proteins and 13,000 phosphopeptides in an experiment investigating similarities and differences between hES and iPS cells that may affect the use of iPS cells for research and therapeutic purposes.