Nanoparticle probes for quantifying supramolecular determinants of biosurface affinity.

Interactions between macromolecular systems and biosurfaces are complicated by both the complexity of these multivalent interactions and challenges in quantifying affinities. A library of gold nanoparticles (AuNPs) as multivalent probes is used to quantify biosurface affinity, using hair as a model targeted substrate.

Phage-protease-peptide: a novel trifecta enabling multiplex detection of viable bacterial pathogens.

Bacteriophages represent rapid, readily targeted, and easily produced molecular probes for the detection of bacterial pathogens. Molecular biology techniques have allowed researchers to make significant advances in the bioengineering of bacteriophage to further improve speed and sensitivity of detection. Despite their host specificity, bacteriophages have not been meaningfully leveraged in multiplex detection of bacterial pathogens. We propose a proof-of-principal phage-based scheme to enable multiplex detection. Our scheme involves bioengineering bacteriophage to carry a gene for a specific protease, which is expressed during infection of the target cell. Upon lysis, the protease is released to cleave a reporter peptide, and the signal detected. Here we demonstrate the successful (i) modification of T7 bacteriophage to carry tobacco etch virus (TEV) protease; (ii) expression of TEV protease by Escherichia coli following infection by our modified T7, an average of 2000 units of protease per phage are produced during infection; and (iii) proof-of-principle detection of E. coli in 3 h after a primary enrichment via TEV protease activity using a fluorescent peptide and using a designed target peptide for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF MS) analysis. This proof-of-principle can be translated to other phage-protease-peptide combinations to enable multiplex bacterial detection and readily adopted on multiple platforms, like MALDI-TOF MS or fluorescent readers, commonly found in labs.

New method to study the effects of peptide sequence on the dissociation energetics of peptide ions.

A new method has been developed to study the dissociation patterns of singly protonated peptides by using a quadrupole ion trap mass spectrometer. The new approach involves using boundary-activated dissociation to characterize the ease of dissociation of peptide ions. Insight can be gained into the effect of specific peptide sequences on the dissociation energetics of protonated peptides. Increased knowledge of the effects of specific sequences on the dissociation patterns of peptide ions should improve the ability to interpret complex spectra from tandem mass spectrometry (MS/MS) experiments. This method has confirmed the previously observed increase in the energy needed for the dissociation of peptide ions containing basic residues. In addition, this technique has revealed the effect of the location of proline residues on the dissociation energetics of peptides with this amino acid.

Boundary-activated dissociation of peptide ions in a quadrupole ion trap.

Boundary-activated dissociation (BAD) of peptides has been investigated as an alternative to the use of resonant excitation to effect collision-induced dissociation in the quadrupole ion trap. BAD's nonresonant excitation mechanism overcomes a major drawback in resonant excitation, namely, the variation of the resonant excitation frequency as a function of ion space charging. As with resonant excitation, the pulsed introduction of heavy gases (argon, xenon) extends the applicability of BAD when tandem mass spectrometry is performed on peptide ions. The presence of heavy gases during ion activation allows greater internal energy deposition and also enables BAD to be performed at much lower trapping field strengths (lower q values) than previously reported for this technique. This extends the mass range over which product ions can be collected.

Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap.

Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b4 ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a4 product ions that are formed directly from the protonated molecule (M + H)+ depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studies here lower series b ions (e.g., b3) arise from direct dissociation of higher series b ions (e.g., b4) only about 50% of the time.

Correlation of kinetic energy losses in high-energy collision-induced dissociation with observed peptide product ions.

In collision-induced dissociation, some of an incident parent ion's kinetic energy is converted into internal energy upon collision with a neutral target. The kinetic energy lost is related to the amount of internal energy deposited into any individual ion. To see dissociations of different critical energies on the same time scale, different amounts of internal energy need to be deposited. This should be reflected in the kinetic energy lost by the parent ion in the formation of different product ions. Variable amounts of energy loss in the formation of different peptide product ions are reported here. It is seen that different product ion types (b, y, a) show ordered patterns of energy losses. A greater energy loss is observed for the formation of b-type product ions than for y-type, and even greater energy losses are observed for the formation of a-type product ions. A very good correlation between ion type energy loss and ion mass is observed. Thus, measuring the energy losses in the formation of product ions may provide a means for classifying the product ion type.

Strategy for pulsed ionization methods on a sector mass spectrometer.

A method to help facilitate efficient implementation of pulsed ionization methods on a double-focusing sector mass spectrometer is described here. This method involves the addition of an inductive detector between the electric and magnetic sectors. The inductive detector will allow a crude, but complete time-of-flight mass spectrum to be acquired with as little as a single laser shot, thereby avoiding the necessity of sequentially compiling limited mass ranges as has been done previously. Mass analysis by the complete sector instrument can be performed simultaneously with the time-of-flight analysis.

Effects of heavy gases on the tandem mass spectra of peptide ions in the quadrupole ion trap.

Heavy gases (xenon, argon, krypton, methane) have been used to improve the performance of the quadrupole ion trap when performing collision-induced dissociation on peptides. MS/MS spectra reveal that increased amounts of internal energy can be deposited into peptide ions and more structural information can be obtained. Specifically, the pulsed introduction of the heavy gases (as reported previously by Doroshenko, V. M.; Cotter, R. J. Anal. Chem. 1996, 68, 463) provides greater energy deposition without the deleterious effects that static pressures of heavy gas have on spectra. Internal energy deposition as indicated by a qualitative evaluation of MS/MS spectra shows pulsed introduction of heavy gases enables ions to obtain more internal energy than possible by using static pressures of the same heavy gases. A linear correlation is observed between the percentage of heavy gas added and the ratio of product ions used to reflect internal energy deposition. Results here also show that upon pulsed introduction of heavy gases, empirical optimization of a single frequency resonant excitation signal is no longer needed to obtain good MS/MS spectrometry efficiency. The presence of many low mass-to-charge ratio ions and the absence of side chain cleavages in the MS/MS spectra of peptides suggests that the propensity for consecutive fragmentations is increased with the pulsed introduction of heavy gases. In addition, by varying the delay time between introduction of the gas and application of the resonant excitation signal, the amount of fragmentation observed in MS/MS spectra can be changed.