Collision-Induced Dissociation Of Dipeptides In Negative Ion Electrospray Ionization Tandem Mass Spectrometry

This purpose of this project was to investigate the collision-induced dissociation of dipeptides in negative ion electrospray ionization tandem mass spectrometry, with a focus on the mechanism of the production of imidazole-type fragments not previously reported from the fragmentation of the dipeptides being studied. The majority of the dipeptides studied were alanine N-terminal or serine C-terminal dipeptides. All dipeptides were dissolved in 50:50 methanol:water, 3 mM ammonium formate. Collision-induced dissociation in the collision cell of a triple quadrupole mass spectrometer was used to fragment [M-H]- precursor ions. Accurate mass measurements confirmed the molecular formula of the imidazole-type fragments. Further MS/MS studies were performed to provide information about the fragmentation mechanism for the formation of the imidazole-type fragments. The m/z values of intermediate ions in the formation of the imidazole-type fragments were confirmed through second-generation product ion scans and precursor ion scans. More sophisticated instrumentation will be required to further probe the structure of the intermediate ions.

A Computational Analysis of the Collision-Induced Dissociation Mechanisms of the Dipeptide Glycine-Serine Under Mass Spectrometry

Collision-induced dissociation (CID) of peptides using tandem mass spectrometry (MS) has been used to determine the identity of peptides and other large biological molecules. Mass spectrometry (MS) is a useful tool for determining the identity of molecules based on their interaction with electromagnetic fields. If coupled with another method like infrared (IR) vibrational spectroscopy, MS can provide structural information, but in its own right, MS can only provide the mass-to-charge (m/z) ratio of the fragments produced, which may not be enough information to determine the mechanism of the collision-induced dissociation (CID) of the molecule. In this case, theoretical calculations provide a useful companion for MS data and yield clues about the energetics of the dissociation. In this study, negative ion electrospray tandem MS was used to study the CID of the deprotonated dipeptide glycine-serine (Gly-Ser). Though negative ion MS is not as popular a choice as positive ion MS, studies by Bowie et al. show that it yields unique clues about molecular structure which complement positive ion spectroscopy, such as characteristic fragmentations like the loss of formaldehyde from the serine residue.2 The increase in the collision energy in the mass spectrometer alters the flexibility of the dipeptide backbone, enabling isomerizations (reactions not resulting in a fragment loss) and dissociations to take place. The mechanism of the CID of Gly-Ser was studied using two computational methods, B3LYP/6-311+G* and M06-2X/6-311++G**. The main pathway for molecular dissociation was analyzed in 5 conformers in an attempt to verify the initial mechanism proposed by Dr. James Swan after examination of the MS data. The results suggest that the loss of formaldehyde from serine, which Bowie et al. indicates is a characteristic of the presence of serine in a protein residue, is an endothermic reaction that is made possible by the conversion of the translational energy of the ion into internal energy as the ion collides with the inert collision gas. It has also been determined that the M06-2X functional¿s improved description of medium and long-range correlation makes it more effective than the B3LYP functional at finding elusive transition states. M06-2X also more accurately predicts the energy of those transition states than does B3LYP. A second CID mechanism, which passes through intermediates with the same m/z ratio as the main pathway for molecular dissociation, but different structures, including a diketopiperazine intermediate, was also studied. This pathway for molecular dissociation was analyzed with 3 conformers and the M06-2X functional, due to its previously determined effectiveness. The results suggest that the latter pathway, which meets the same intermediate masses as the first mechanism, is lower in overall energy and therefore a more likely pathway of dissociation than the first mechanism.

Catastrophic Flooding In North-Central Pennsylvania: Geomorphic Findings From The September 2011 Event And Their Significance To

Tropical Storm Lee produced 25-36 cm of rainfall in north-central Pennsylvania on September 4th through 8th of 2011. Loyalsock Creek, Muncy Creek, and Fishing Creek experienced catastrophic flooding resulting in new channel formation, bank erosion, scour of chutes, deposition/reworking of point bars and chute bars, and reactivation of the floodplain. This study was created to investigate aspects of both geomorphology and sedimentology by studying the well-exposed gravel deposits left by the flood, before these features are removed by humans or covered by vegetation. By recording the composition of gravel bars in the study area and creating lithofacies models, it is possible to understand the 2011 flooding. Surficial clasts on gravel bars are imbricated, but the lack of imbrication and high matrix content of sediments at depth suggests that surface imbrication of the largest clasts took place during hyperconcentrated flow (40-70% sediment concentration). The imbricated clasts on the surface are the largest observed within the bars. The lithofacies recorded are atypical for mixed-load stream lithofacies and more similar to glacial outburst flood lithofacies. This paper suggests that the accepted lithofacies model for mixed-load streams with gravel bedload may not always be useful for interpreting depositional systems. A flume study, which attempted to duplicate the stratigraphy recorded in the field, was run in order to better understand hyperconcentrated flows in the study area. Results from the study in the Bucknell Geology Flume Laboratory indicate that surficial imbrication is possible in hyperconcentrated conditions. After flooding the flume to entrain large amounts of sand and gravel, deposition of surficially imbricated gravel with massive or upward coarsening sedimentology occurred. Imbrication was not observed at depth. These experimental flume deposits support our interpretation of the lithofacies discovered in the field. The sizes of surficial gravel bar clasts show clear differences between chute and point bars. On point bars, gravels fine with increasing distance from the channel. Fining also occurs at the downstream end of point bars. In chute deposits, dramatic fining occurs down the axis of the chute, and lateral grain sizes are nearly uniform. Measuring the largest grain size of sandstone clasts at 8-11 kilometer intervals on each river reveals anomalies in the downstream fining trends. Gravel inputs from bedrock outcrops, tributaries, and erosion of Pleistocene outwash terraces may explain observed variations in grain size along streams either incised into the Appalachian Plateau or located near the Wisconsinan glacial boundary. Atomic Mass Spectrometry (AMS) radiocarbon dating of sediment from recently scoured features on Muncy Creek and Loyalsock Creek returned respective ages of 500 BP and 2490 BP. These dates suggest that the recurrence interval of the 2011 flooding may be several hundred to several thousand years. This geomorphic interval of recurrence is much longer then the 120 year interval calculated by the USGS using historical stream gauge records.