Protein identification via surface-induced dissociation in an FT-ICR mass spectrometer and a patchwork sequencing approach

Surface-induced dissociation (SID) and collision-induced dissociation (CID) are ion activation techniques based on energetic collisions with a surface or gas molecule, respectively. One noticeable difference between CID and SID is that SID does not require a collision gas for ion activation and is, therefore, directly compatible with the high vacuum requirement of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Eliminating the introduction of collision gas into the ICR cell for collisional activation dramatically shortens the acquisition time for MS/MS experiments, suggesting that SID could be utilized for high-throughput MS/MS studies in FT-ICR MS. We demonstrate for the first time the utility of SID combined with FT-ICR MS for protein identification. Tryptic digests of standard proteins were analyzed using a hybrid 6-tesla FT-ICR mass spectrometer with SID and CID capabilities. SID spectra of mass-selected singly and doubly charged peptides were obtained using a diamond-coated target mounted at the rear trapping plate of the ICR cell. The broad internal energy distribution deposited into the precursor ion following collision with the diamond surface allowed a variety of fragmentation channels to be accessed by SID. Composition and sequence qualifiers produced by SID of tryptic peptides were used to improve the statistical significance of database searches. Protein identification MASCOT scores obtained using SID were comparable or better than scores obtained using sustained off-resonance irradiation collision-induced dissociation (SORI-CID), the conventional ion activation technique in FT-ICR MS.     

Modification of indium-tin oxide electrodes with thiophene copolymer thin films: optimizing electron transfer to solution probe molecules

We describe the modification of indium-tin oxide (ITO) electrodes via the chemisorption and electropolymerization of 6-{2,3-dihydrothieno[3,4-b]-1.4-dioxyn-2-yl methoxy}hexanoic acid (EDOTCA) and the electrochemical co-polymerization of 3,4-ethylenedioxythiophene (EDOT) and EDOTCA to form ultrathin films that optimize electron-transfer rates to solution probe molecules. ITO electrodes were first activated using brief exposure to strong haloacids, to remove the top approximately 8 nm of the electrode surface, followed by immediate immersion into a 50:50 EDOT/EDOTCA co-monomer solution. Potential step electrodeposition for brief deposition times was used to grow copolymer films of thickness 10-100 nm. The composition of these copolymer films was characterized by solution depletion studies of the monomers and atomic force microscopy (AFM), X-ray photoelectron spectroscopy, and Fourier transform infrared spectroscopy (reflection-absorption infrared spectroscopy (RAIRS)) of the product films. The spectroscopic data suggest that the composition of the copolymer approaches 80% EDOTCA when electropolymerization occurs from concentrated (10 mM) solutions. AFM characterization shows that electrodeposited poly(EDOT)/poly(EDOTCA) (PEDOT/PEDOTCA) films are quite smooth, with texturing on the nanometer scale. RAIRS studies indicate that these films consist of a combination of EDOTCA units with noninteracting -COOH groups and adjacent hydrogen-bonded -COOH groups. The EDOTCA-containing polymer chains appear to grow as columnar clusters from specific regions, oriented nearly vertically to the substrate plane. As they grow, these columnar clusters overlap to form a nearly continuous redox active polymer film. ITO activation and formation of these copolymer films enhances the electroactive fraction of the electrode surface relative to a nonactivated, unmodified "blocked" ITO electrode. Outer-sphere solution redox probes (dimethylferrocene) give standard rate coefficients, kS > or = 0.4 cm.s-1, at 10 nm thick copolymer films of PEDOT/PEDOTCA, which is 3 orders of magnitude greater than that on the unmodified ITO surface and approaches the values for kS seen on clean gold surfaces.     

Carbon dioxide and ammonia detection using 2 μm diode laser based quartz-enhanced photoacoustic spectroscopy

Quartz-enhanced photoacoustic spectroscopy was employed for trace gas concentration measurements of CO₂ and NH₃ using a continuous wave thermoelectrically cooled, distributed feedback diode laser operating at 2 μm. A normalized noise equivalent absorption coefficient, NNEA(1σ)=1.4×10^-8 cm^-1W/ was obtained for CO₂ using the R18 line of the 2ν₁+ν₃ band at 4991.26 cm^-1. This corresponds to minimum detection limit (1σ) of 18 parts per million (ppm) for a 1 s lock-in time constant. The influence of the H₂O presence in the sample gas mixture on the CO₂ sensor performance was investigated. Ammonia detection was performed using the ^P P ₆(6)_S line of the ν₃+ν₄ band at 4986.99 cm^-1. A detection limit (1σ) of 3 ppm for NH₃ concentration with a 1 s lock-in time constant was achieved. This results in a normalized noise equivalent absorption of NNEA(1σ)=8.9×10^-9 cm^-1W/. PACS 82.80.Kq; 46.62.Fi; 42.55.Px