Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications

Abstract

Despite major advantages in the field of proteomics, the analysis of PTMs still poses a major challenge; thus far, preventing insights into the role and regulation of protein networks. Additionally, top-down sequencing of proteins is another powerful approach to reveal comprehensive information for biological function. A commonly used fragmentation technique in MS-based peptide sequencing is CID. As CID often fails in PTM-analysis and performs best on doubly-charged, short and middle-sized peptides, confident peptide identification may be hampered. A newly developed fragmentation technique, namely electron transfer dissociation (ETD), supports both, PTM- and top-down analysis, and generally results in more confident identification of long, highly charged or modified peptides. The following review presents the theoretical background of ETD and its technical implementation in mass analyzers. Furthermore, current improvements of ETD and approaches for the PTM-analysis and top-down sequencing are introduced. Alternating both fragmentation techniques, ETD and CID, increases the amount of information derived from peptide fragmentation, thereby enhancing both, peptide sequence coverage and the confidence of peptide and protein identification.

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

“…In particular, this approach has the advantage of preserving unstable side-chain modifications during fragmentation [11,28]. Several different instrumental approaches have been developed to utilize electrons for fragmentation, including ECD in FT-ICR mass spectrometers [29], ECD in radio-frequency linear ion trap mass spectrometers [30], and electron-transfer ion/ion reactions in quadrupole/linear ion trap mass spectrometers [31], hybrid quadrupole-hexapole FT-ICRs [32], and hybrid linear ion trap-Orbitrap mass spectrometers [33].…”

Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides

“…It has been reported that attachment of an electron to multiply protonated phosphopeptides caused backbone fragmentations while preserving the phosphate group in the fragments [4]. This feature has been utilized in studies aimed at the localization of phosphorylated residues in peptides produced by enzymatic digestion of proteins [5][6][7][8][9][10][11][12]. However, it has also been reported that the presence of phosphorylated serine residues hampered backbone dissociations of several synthetic peptides [16].…”

“…E lectron-based methods such as electron capture dissociation (ECD) [1] and electron transfer dissociation (ETD) [2,3], which are collectively referred to as ExD, have been shown to be suitable for the analysis of peptides posttranslationally modified by phosphorylation [4][5][6][7][8][9][10][11][12], sulfation [13], or glycosylation [14,15]. It has been reported that attachment of an electron to multiply protonated phosphopeptides caused backbone fragmentations while preserving the phosphate group in the fragments [4].…”

Comprehensive Mass Spectrometric Mapping of the Hydroxylated Amino Acid residues of the α1(V) Collagen Chain

“…Because of high ␣1(V) Pro content and decreased efficacy of ETD-induced cleavage of Pro N-C ␣ bonds, ETD MS 2 analyses occasionally did not provide sufficient numbers of sequenceinformative product ions to permit PTM localization (67). To complement ETD data, data were also acquired utilizing HCD collected at different collision energies.…”