Project description:The normalized cross-correlation (NCC), usually its 2D version, is routinely encountered in template matching algorithms, such as in facial recognition, motion-tracking, registration in medical imaging, etc. Its rapid computation becomes critical in time sensitive applications. Here I develop a scheme for the computation of NCC by fast Fourier transform that can favorably compare for speed efficiency with other existing techniques and may outperform some of them given an appropriate search scenario.
Project description:The theory of the continuous two-dimensional (2D) Fourier Transform in polar coordinates has been recently developed but no discrete counterpart exists to date. In the first part of this two-paper series, we proposed and evaluated the theory of the 2D Discrete Fourier Transform (DFT) in polar coordinates. The theory of the actual manipulated quantities was shown, including the standard set of shift, modulation, multiplication, and convolution rules. In this second part of the series, we address the computational aspects of the 2D DFT in polar coordinates. Specifically, we demonstrate how the decomposition of the 2D DFT as a DFT, Discrete Hankel Transform and inverse DFT sequence can be exploited for coding. We also demonstrate how the proposed 2D DFT can be used to approximate the continuous forward and inverse Fourier transform in polar coordinates in the same manner that the 1D DFT can be used to approximate its continuous counterpart.
Project description:A multiplexed tandem mass spectrometry (MS/MS) technique known as iterative accumulation multiplexing (IAM) has been implemented on a hybrid quadrupole Fourier transform ion cyclotron resonance mass spectrometer (Q-FTICR-MS). The IAM experiment resulted in obtaining MS/MS spectra for six analytes in two MS/MS experiments while characteristic resolving power and mass measurement accuracies were maintained. Parent-product ion correlations were graphically represented in a "ratiogram" where each product ion is encoded with a ratio unique to the parent ion from which it was formed. This is the first example of multiplexed MS on a FTICR instrument where the ions are encoded externally to the ICR cell. By performing the encoding external to the ICR cell, one set of ions can be encoded while the previous set of ions is being analyzed in the cell, maximizing the use of the continuous ion current emanating from the electrospray ionization source.
Project description:INTRODUCTION:Direct injection Fourier-transform mass spectrometry (FT-MS) allows for the high-throughput and high-resolution detection of thousands of metabolite-associated isotopologues. However, spectral artifacts can generate large numbers of spectral features (peaks) that do not correspond to known compounds. Misassignment of these artifactual features creates interpretive errors and limits our ability to discern the role of representative features within living systems. OBJECTIVES:Our goal is to develop rigorous methods that identify and handle spectral artifacts within the context of high-throughput FT-MS-based metabolomics studies. RESULTS:We observed three types of artifacts unique to FT-MS that we named high peak density (HPD) sites: fuzzy sites, ringing and partial ringing. While ringing artifacts are well-known, fuzzy sites and partial ringing have not been previously well-characterized in the literature. We developed new computational methods based on comparisons of peak density within a spectrum to identify regions of spectra with fuzzy sites. We used these methods to identify and eliminate fuzzy site artifacts in an example dataset of paired cancer and non-cancer lung tissue samples and evaluated the impact of these artifacts on classification accuracy and robustness. CONCLUSION:Our methods robustly identified consistent fuzzy site artifacts in our FT-MS metabolomics spectral data. Without artifact identification and removal, 91.4% classification accuracy was achieved on an example lung cancer dataset; however, these classifiers rely heavily on artifactual features present in fuzzy sites. Proper removal of fuzzy site artifacts produces a more robust classifier based on non-artifactual features, with slightly improved accuracy of 92.4% in our example analysis.
Project description:A new instrument configuration for native ion mobility-mass spectrometry (IM-MS) is described. Macromolecule ions are generated by using a static ESI source coupled to an RF ion funnel, and these ions are then mobility and mass analyzed using a periodic focusing drift tube IM analyzer and an Orbitrap mass spectrometer. The instrument design retains the capabilities for first-principles determination of rotationally averaged ion-neutral collision cross sections and high-resolution measurements in both mobility and mass analysis modes for intact protein complexes. Operation in the IM mode utilizes FT-IMS modes (originally described by Knorr ( Knorr , F. J. Anal. Chem . 1985 , 57 ( 2 ), 402 - 406 )), which provides a means to overcome the inherent duty cycle mismatch for drift tube (DT)-IM and Orbitrap mass analysis. The performance of the native ESI-FT-DT-IM-Orbitrap MS instrument was evaluated using the protein complexes Gln K (MW 44 kDa) and streptavidin (MW 53 kDa) bound to small molecules (ADP and biotin, respectively) and transthyretin (MW 56 kDa) bound to thyroxine and zinc.
Project description:The pharmaceutical industry's interest in monoclonal antibodies (mAbs) and their derivatives has spurred rapid growth in the commercial and clinical pipeline of these effective therapeutics. The complex micro-heterogeneity of mAbs requires in-depth structural characterization for critical quality attribute assessment and quality assurance. Currently, mass spectrometry (MS)-based methods are the gold standard in mAb analysis, primarily with a bottom-up approach in which immunoglobulins G (IgGs) and their variants are digested into peptides to facilitate the analysis. Comprehensive characterization of IgGs and the micro-variants remains challenging at the proteoform level. Here, we used both top-down and middle-down MS for in-depth characterization of a human IgG1 using ultra-high resolution Fourier transform MS. Our top-down MS analysis provided characteristic fingerprinting of the IgG1 proteoforms at unit mass resolution. Subsequently, the tandem MS analysis of intact IgG1 enabled the detailed sequence characterization of a representative IgG1 proteoform at the intact protein level. Moreover, we used the middle-down MS analysis to characterize the primary glycoforms and micro-variants. Micro-variants such as low-abundance glycoforms, C-terminal glycine clipping, and C-terminal proline amidation were characterized with bond cleavages higher than 44% at the subunit level. By combining top-down and middle-down analysis, 76% of bond cleavage (509/666 amino acid bond cleaved) of IgG1 was achieved. Taken together, we demonstrated the combination of top-down and middle-down MS as powerful tools in the comprehensive characterization of mAbs.
Project description:We present a subspace method that accelerates data acquisition using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry imaging (MSI). For MSI of biological tissue samples, there is a finite number of heterogeneous tissue types with distinct chemical profiles that introduce redundancy in the high-dimensional measurements. Our subspace model exploits the redundancy in data measured from whole-slice tissue samples by decomposing the transient signals into linear combinations of a set of basis transients with the desired spectral resolution. This decomposition allowed us to design a strategy that acquires a subset of long transients for basis determination and short transients for the remaining pixels, drastically reducing the acquisition time. The computational reconstruction strategy can maintain high-mass-resolution and spatial-resolution MSI while providing a 10-fold improvement in throughput. We validated the capability of the subspace model using a rat sagittal brain slice imaging data set. Comprehensive evaluation of the quality of the mass spectral and ion images demonstrated that the reconstructed data produced by the reported method required only 15% of the typical acquisition time and exhibited both qualitative and quantitative consistency when compared to the original data. Our method enables either higher sample throughput or higher-resolution images at similar acquisition lengths, providing greater flexibility in obtaining FT-ICR MSI measurements.
Project description:Fourier-transform spectroscopy (FTS) has been widely used as a standard analytical technique over the past half-century. FTS is an autocorrelation-based technique that is compatible with both temporally coherent and incoherent light sources, and functions as an active or passive spectrometer. However, it has been mostly used for static measurements due to the low scan rate imposed by technological restrictions. This has impeded its application to continuous rapid measurements, which would be of significant interest for a variety of fields, especially when monitoring of non-repeating or transient complex dynamics is desirable. Here, we demonstrate highly efficient FTS operating at a high spectral acquisition rate with a simple delay line based on a dynamic phase-control technique. The independent adjustability of phase and group delays allows us to achieve the Nyquist-limited spectral acquisition rate over 10,000 spectra per second, while maintaining a large spectral bandwidth and high resolution. We also demonstrate passive spectroscopy with an incoherent light source.
Project description:The relationship of magnetic field strength and Fourier transform ion cyclotron resonance mass spectrometry performance was tested using three instruments with the same design but different fields of 4.7, 7, and 9.4 tesla. We found that the theoretically predicted "transformative" effects of magnetic field are indeed observed experimentally. The most striking effects were that mass accuracy demonstrated approximately second to third order improvement with the magnetic field, depending upon the charge state of the analyte, and that peak splitting, which prohibited automated data analysis at 4.7 T, was not observed at 9.4 T.