Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome.
Better understanding how cells are regulated and adapt to their environment based on the reversible phosphorylation of proteins is a key question of current molecular and systems biology research. In this study, an advanced mass spectrometry based approach leveraging the electron transfer dissociation (ETD) technique in combination with CID using a linear ion trap mass spectrometer is described. The technique was applied, for the first time, to the identification of phosphorylated peptides isolated from the Drosophila melanogaster Kc167 cell line. We demonstrate that the method is particularly useful for the characterization of large phosphopeptides, including those with multiple phosphorylation sites, as extensive series of c' and z fragment-ions were observed. Finally, we have applied a directed tandem mass spectrometric workflow using inclusion lists to increase the number of identified peptides.
Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland. domon@imsb.biol.ethz.ch
Bruno
B
Domon
Bernd
B
Bodenmiller
Christine
C
Carapito
Zhiqi
Z
Hao
Andreas
A
Huehmer
Ruedi
R
Aebersold
D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D002853:Chromatography, Liquid; D029721:Drosophila Proteins / Q000737:chemistry*; D004331:Drosophila melanogaster / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides; D010748:Phosphopeptides / Q000737:chemistry*; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics; D053719:Tandem Mass Spectrometry / Q000379:methods*
D029721:Drosophila Proteins; D010455:Peptides; D010748:Phosphopeptides; D010750:Phosphoproteins; D020543:Proteome