Simultaneous collision induced dissociation of the charge reduced parent ion during electron capture dissociation

Elucidating the sequence of intact bioactive peptides by using electron capture dissociation and hot electron capture dissociation in a linear radio-frequency quadrupole ion trap

RATIONALE

Electron capture dissociation (ECD) is useful tool for sequencing of peptides and proteins with post-translational modifications. To increase the sequence coverage for peptides and proteins, it is important to develop ECD device with high fragmentation efficiency.

METHODS

Sequence analysis of intact undigested bioactive peptides (3000-5000 Da) was performed by use of electron capture dissociation (rf-ECD) and collision-induced dissociation (CID) in a linear radio-frequency quadrupole ion trap that was coupled to a time-of-flight mass spectrometer. We applied rf-ECD, hot rf-ECD (rf-ECD with high electron energy), and CID for intact bioactive peptide ions of various charge states and evaluated the sequence coverage of their fragment spectra.

RESULTS

Hot rf-ECD produced a higher number of c- and z-type fragment ions of modified peptide ions as electron energy increased in lower charged peptide ions, and sequence coverage greater than 80% was obtained compared with the CID case (40-80%).

CONCLUSIONS

The result indicates that intact bioactive modified peptides (Ghrelin, ANP) were correctly identified by use of hot rf-ECD.

Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.

Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins.

Tandem mass spectrometry strategies for phosphoproteome analysis

Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.

Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer

Shotgun proteomics has been used extensively for characterization of a number of proteomes. High-resolution Fourier transform mass spectrometry (FTMS) has emerged as a powerful tool owing to its high mass accuracy and resolving power. One of its major limitations, however, is that the confidence level of peptide identification and sensitivity cannot be maximized simultaneously. Although it is generally assumed that higher resolution is better for peptide identifications, the precise effect of varying resolution as a parameter on peptide identification has not yet been systematically evaluated. We used the Escherichia coli proteome and a standard 48 protein mix to study the effect of different resolution parameters on peptide identifications in the setting of a shotgun proteomics experiment on an LTQ-Orbitrap mass spectrometer. We observed a higher number of peptide-spectrum matches (PSMs) whenever the MS scan was carried out by FT and the MS/MS in the ion-trap (IT) with the maximum PSMs obtained at an MS resolution of 30,000. In contrast, when samples were analyzed by FT for both MS and MS/MS, the number of PSMs was significantly lower (approximately 40% compared with FT-IT experiments) with the maximum PSMs obtained when both the MS and MS/MS resolution were set to 15,000. Thus, a 15K-15K resolution setting may provide the best compromise for studies where both speed and accuracy such as high-throughput post-translational analysis and de novo sequencing are important. We hope that our study will allow researchers to choose between different resolution parameters to achieve their desired results from proteomic analyses.