Peptide fragmentation induced by radicals at atmospheric pressure.

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essential atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to electron capture dissociation/electron transfer dissociation (ECD/ETD), along with the y-/b-type fragments that are specific to collision-activated dissociation (CAD). In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer.

Comparative performance of tripole and quadrupole ion guides at elevated pressure.

This study presents the first practical demonstration of an operational tripole ion guide. The transmission was measured for both the tripole and quadrupole ion guides at 1 Torr pressure. It was found that the quadrupole provides 2.

Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling.

Bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. However, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. The modification complement of a protein can best be elucidated by analyzing the intact protein.

Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry.

We describe methods for mass spectrometric identification of heme-containing peptides from c-type cytochromes that contain the CXXCH (X=any amino acid) sequence motif. The heme fragment ion yielded the most abundant MS/MS peak for standard heme-containing peptides with one amino acid difference for both 2+ and 3+ peptide charge states; both sequence and charge affect the extent of heme loss. Application to Shewanella oneidenis demonstrated the utility of this approach for identifying c-type heme-containing peptides from complex proteome samples.

Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel.

We report on the use of a jet disrupter electrode in an electrodynamic ion funnel as an electronic valve to regulate the intensity of the ion beam transmitted through the interface of a mass spectrometer in order to perform automatic gain control (AGC). The ion flux is determined by either directly detecting the ion current on the conductance limiting orifice of the ion funnel or using a short mass spectrometry acquisition. Based upon the ion flux intensity, the voltage of the jet disrupter is adjusted to alter the transmission efficiency of the ion funnel to provide a desired ion population to the mass analyzer.

Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry.

In proteomics, effective methods are needed for identifying the relatively limited subset of proteins displaying significant changes in abundance between two samples. One way to accomplish this task is to target for identification by MS/MS only the "interesting" proteins based on the abundance ratio of isotopically labeled pairs of peptides. We have developed the software and hardware tools for online LC-FTICR MS/MS studies in which a set of initially unidentified peptides from a proteome analysis can be selected for identification based on their distinctive changes in abundance following a "perturbation".

Collisional activation of ions in RF ion traps and ion guides: the effective ion temperature treatment.

Ion transfer and storage using inhomogeneous radio frequency (RF) electric fields in combination with gas-assisted ion cooling and focusing constitutes one of the basic techniques in mass spectrometry today. The RF motion of ions in the bath gas environment involves a large number of ion-neutral collisions that leads to the internal activation of ions and their effective "heating" (when a thermal distribution of internal energies results). The degree of ion activation required in various applications may range from a minimum level (e.

Tailored noise waveform/collision-induced dissociation of ions stored in a linear ion trap combined with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry.

A new collision-induced dissociation (CID) technique based on broadband tailored noise waveform (TNW) excitation of ions stored in a linear ion trap has been developed. In comparison with the conventional sustained off-resonance irradiation (SORI) CID method commonly used in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), this MS/MS technique increases throughput by eliminating the long pump-down delay associated with gas introduction into the high vacuum ICR cell region. In addition, the TNW-CID method speeds spectrum acquisition since it does not require Fourier transformation, calculation of resonant frequencies and generation of the excitation waveforms.

Suppression of the lower charge state ions in the external accumulation RF multipole with a reduced trapping DC potential.

Radio frequency (RF) multipoles are increasingly used in mass spectrometry as two-dimensional ion traps for ion accumulation and preselection. It was reported recently that ions having lower charge states, in particular singly charged ions, can be efficiently removed from such an ion trap when reduced DC trapping voltages are applied. This procedure can be useful for removing singly charged species contributing chemical noise to mass spectra of complex biomolecular samples, e.