The effects of abundant plasma protein depletion on global glycan profiling using NanoLC FT-ICR mass spectrometry

We report the results of abundant plasma protein depletion on the analysis of underivatized N-linked glycans derived from plasma proteins by nanoLC Fourier-transform ion cyclotron resonance mass spectrometry. N-linked glycan profiles were compared between plasma samples where the six most abundant plasma proteins were depleted (n = 3) through a solid-phase immunoaffinity column and undepleted plasma samples (n = 3). Three exogenous glycan standards were spiked into all samples which allowed for normalization of the N-glycan abundances. The abundances of 20 glycans varying in type, structure, composition, and molecular weight (1,200–3,700 Da) were compared between the two sets of samples. Small fucosylated non-sialylated complex glycans were found to decrease in abundance in the depleted samples (greater than or equal to tenfold) relative to the undepleted samples. Protein depletion was found to marginally effect (less than threefold) the abundance of high mannose, hybrid, and large highly sialylated complex species. The significance of these findings in terms of future biomarker discovery experiments via global glycan profiling is discussed.     

Clifford Fourier Transformation and Uncertainty Principle for the Clifford Geometric Algebra Cl 3,0

First, the basic concept of the vector derivative in geometric algebra is introduced. Second, beginning with the Fourier transform on a scalar function we generalize to a real Fourier transform on Clifford multivector-valued functions Third, we show a set of important properties of the Clifford Fourier transform on Cl_3,0 such as differentiation properties, and the Plancherel theorem. Finally, we apply the Clifford Fourier transform properties for proving an uncertainty principle for Cl_3,0 multivector functions.     

Minimum dissipative relaxed states in toroidal plasmas

Relaxation of toroidal discharges is described by the principle of minimum energy dissipation together with the constraint of conserved global helicity. The resulting Euler-Lagrange equation is solved in toroidal coordinates for an axisymmetric torus by expressing the solutions in terms of Chandrasekhar-Kendall (C-K) eigenfunctions analytically continued in the complex domain. The C-K eigenfunctions are obtained as hypergeometric functions that are solutions of scalar Helmholtz equation in toroidal coordinates in the large aspect-ratio approximation. Equilibria are constructed by assuming the current to vanish at the edge of plasma. For the m=0, n=0 (m and n are the poloidal and toroidal mode numbers respectively) relaxed states, the magnetic field, current, q (safety factor) and pressure profiles are calculated for a given value of aspect-ratio of the torus and for different values of the eigenvalue λ _{r 0}. The new feature of the present model is that solutions allow for both tokamak as well as RFP-like behaviour with increase in the values of λ _{r 0}, which is related directly to volt-sec in the experiment.     

De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics

We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1?min, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from ?C0.1776?±?0.0010?m/z to 0.0078?±?0.0006?m/z after calibration (avg?±?95?% confidence interval). The precision in mass measurement was improved due to the correction of non-linear variation in mass measurement accuracy across the m/z range.     

Detection of Attomole Amounts of Analyte by Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) Determined Using Fluorescence Spectroscopy

We report the use of fluorescence spectroscopy to investigate the amount of material removed from a PTFE surface and detected during desorption electrospray ionization (DESI) mass spectrometry measurements. The fluorescence intensity before and after DESI analysis of rhodamine 6G is used to determine the amount of material removed from the surface per mass spectrum. Calculations indicate low attomole amounts are removed per linear ion trap mass spectrum.     

Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer

We report a direct comparison of the mass measurement accuracies (MMAs) obtained on different mass spectrometry instrument types; a magnetic sector as the 'gold standard' and an electrospray ionization time-of-flight (ESI-TOF) instrument. Sixty samples, obtained from the Department of Chemistry at North Carolina State University, were analyzed on each instrument. Data are presented and compared between the different instruments. The average absolute MMAs achieved for the magnetic sector and Agilent ESI-TOF mass spectrometers were 3.0 and 1.1 ppm, respectively.