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Peptide Fragmentation (peptide + fragmentation)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Fragmentation pathways of protonated peptides

MASS SPECTROMETRY REVIEWS, Issue 4 2005
Béla Paizs
Abstract The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the ,mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the ,pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:508,548, 2005 [source]

Proteomics by FTICR mass spectrometry: Top down and bottom up

MASS SPECTROMETRY REVIEWS, Issue 2 2005
Bogdan Bogdanov
Abstract This review provides a broad overview of recent Fourier transform ion cyclotron resonance (FTICR) applications and technological developments relevant to the field of proteomics. Both the "bottom up" (peptide level) and "top down" (intact protein level) approaches are discussed and illustrated with examples. "Bottom up" topics include peptide fragmentation, the accurate mass and time (AMT) tag approach and dynamic range extension technology, aspects of quantitative proteomics measurements, post-translational modifications, and developments in FTICR operation software focused on peptide and protein identification. Topics related to the "top down" approach include various aspects of high mass measurements, protein tandem mass spectrometry, methods for the study of protein conformations, and protein complexes as well as advanced technologies that may become of practical utility in the coming years. Finally, early examples of the integration of both FTICR approaches to biomedical proteomics applications are presented, along with an outlook for future directions. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:168,200, 2005 [source]

Balancing robust quantification and identification for iTRAQ: Application of UHR-ToF MS

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 11 2010
Saw Yen Ow
Abstract iTRAQ reagents allow the simultaneous multiplex identification and quantification of a large number of proteins. Success depends on effective peptide fragmentation in order to generate both peptide sequence ions (higher mass region, 150,2200,m/z) and reporter ions (low mass region, 113,121,m/z) for protein identification and relative quantification, respectively. After collision-induced dissociation, the key requirements to achieve a good balance between the high and low m/z ions are effective ion transmission and detection across the MS/MS mass range, since the ion transmission of the higher m/z range competes with that of the low m/z range. This study describes an analytical strategy for the implementation of iTRAQ on maXis UHR-Qq-ToF instruments, and discusses the impact of adjusting the MS/MS ion transmission parameters on the quality of the overall data sets. A technical discussion highlights a number of maXis-specific parameters, their impact of quantification and identification, and their cross-interactions. [source]

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

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 21 2008
Julia Wiesner
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. [source]