FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Comparison of infrared-excited up-converting phosphors and europium nanoparticles as labels in a two-site immunoassay

Research in the field of immunoassays and labels used in the detection has been recently focused on particulate reporters, which possess very high specific activity that excludes the label as a sensitivity limiting factor. However, the large size and shape of the particulate labels may produce additional problems to immunoassay performance. The aim of this work was to study with two identical non-competitive two-site immunoassays whether up-converting phosphor (UCP) particles are comparable in performance with europium(III) chelate-dyed nanoparticles as particulate labels. In addition we strived to verify the common assumption of the photostability of up-converting phosphor particles supporting their potential applicability in imaging. Detection limits in two-site immunoassay for free prostate-specific antigen (free-PSA) were 0.53 ng L⁻¹ and 1.3 ng L⁻¹ using two different up-converting phosphors and 0.16 ng L⁻¹ using europium(III) nanoparticle. Large size distribution and non-specific binding of up-converting phosphor particles caused assay variation in low analyte concentrations and limited the analytical detection limit. The non-specific binding was the major factor limiting the analytical sensitivity of the immunoassay. The results suggests the need for nanoscaled and uniformely sized UCP-particles to increace the sensitivity and applicability of up-converting phosphor particles. Anti-Stokes photoluminescence of up-converting phosphor particles did not photobleach when measured repeatedly, on the contrary, the time-resolved fluorescence of europium nanoparticles photobleached relatively rapidly.     

A Bayesian molecular interaction library

We describe a library of molecular fragments designed to model and predict non-bonded interactions between atoms. We apply the Bayesian approach, whereby prior knowledge and uncertainty of the mathematical model are incorporated into the estimated model and its parameters. The molecular interaction data are strengthened by narrowing the atom classification to 14 atom types, focusing on independent molecular contacts that lie within a short cutoff distance, and symmetrizing the interaction data for the molecular fragments. Furthermore, the location of atoms in contact with a molecular fragment are modeled by Gaussian mixture densities whose maximum a posteriori estimates are obtained by applying a version of the expectation-maximization algorithm that incorporates hyperparameters for the components of the Gaussian mixtures. A routine is introduced providing the hyperparameters and the initial values of the parameters of the Gaussian mixture densities. A model selection criterion, based on the concept of a `minimum message length' is used to automatically select the optimal complexity of a mixture model and the most suitable orientation of a reference frame for a fragment in a coordinate system. The type of atom interacting with a molecular fragment is predicted by values of the posterior probability function and the accuracy of these predictions is evaluated by comparing the predicted atom type with the actual atom type seen in crystal structures. The fact that an atom will simultaneously interact with several molecular fragments forming a cohesive network of interactions is exploited by introducing two strategies that combine the predictions of atom types given by multiple fragments. The accuracy of these combined predictions is compared with those based on an individual fragment. Exhaustive validation analyses and qualitative examples (e.g., the ligand-binding domain of glutamate receptors) demonstrate that these improvements lead to effective modeling and prediction of molecular interactions.     

BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

Building the quality into pellet manufacturing environment--feasibility study and validation of an in-line quantitative near infrared (NIR) method

The present study focuses on the implementation of an in-line quantitative near infrared (NIR) spectroscopic method for determining the active content of pharmaceutical pellets. The first aim was to non-invasively interface a dispersive NIR spectrometer with four realistic particle streams existing in the pellets manufacturing environment. Regardless of the particle stream characteristics investigated, NIR together with Principal Component Analysis (PCA) was able to classify the samples according to their active content. Further, one of these particle stream interfaces was non-invasively investigated with a FT-NIR spectrometer. A predictive model based on Partial Least Squares (PLS) regression was able to determine the active content of pharmaceutical pellets. The NIR method was finally validated with an external validation set for an API concentration range from 80 to 120% of the targeted active content. The prediction error of 0.9% (root mean standard error of prediction, RMSEP) was low, indicating the accuracy of the NIR method. The accuracy profile on the validation results, an innovative approach based on tolerance intervals, demonstrated the actual and future performance of the in-line NIR method. Accordingly, the present approach paves the way for real-time release-based quality system.     

Dizincation of a 2-substituted thiophene: constructing a cage with a [16]crown-4 zincocyclic core

Metal detector: a bowl-shaped nanomolecule (see picture; S yellow, C gray, Zn blue) containing an unprecedented 16-atom [ZnC(3)](4) "anti-crown" ring has been unearthed by isolating a dizincated 2-substituted thiophene intermediate that would normally be hidden in tandem functionalization methodology.     

Photochemical Characterization of Up-Converting Inorganic Lanthanide Phosphors as Potential Labels

We have characterized commercially available up-converting inorganic lanthanide phosphors for their rare earth composition and photoluminescence properties under infrared laser diode excitation. These up-converting phosphors, in contrast to proprietary materials reported earlier, are readily available to be utilized as particulate reporters in various ligand binding assays after grinding to submicron particle size. The laser power density required at 980 nm to generate anti-Stokes photoluminescence from these particulate reporters is significantly lower than required for two-photon excitation. The narrow photoluminescence emission bands at 520–550 nm and at 650–670 nm are at shorter wavelengths and thus totally discriminated from autofluorescence and scattered excitation light even without temporal resolution. Transparent solution of colloidal bead-milled up-converting phosphor nanoparticles provides intense green emission visible to the human eye under illumination by an infrared laser pointer. In this article, we show that the unique photoluminescence properties of the up-converting phosphors and the inexpensive measurement configuration, which is adequate for their sensitive detection, render the up-conversion an attractive alternative to the ultraviolet-excited time-resolved fluorescence of down-converting lanthanide compounds widely employed in biomedical research and diagnostics.     

Trace Element Determination in Diesel Particulates by Total-Reflection X-Ray Fluorescence Analysis

 Particulate matter of Diesel emissions collected from diluted exhaust during standard test runs with two Diesel fuels of different sulfur content was analysed by total-reflection X-ray fluorescence (TXRF). The trace elements determined were S, Ca, Cr, Mn, Fe, Ni, Cu, Zn and Pb. Additionally, some filter materials were tested with respect to their applicability for sample collection. Quartz fibre filters were found to be most suitable, both from a technical and a chemical point of view. A clear reduction of total particulate emissions during the whole test was observed when the fuel with very low sulfur content was used. In addition, it was found that the wear metal content of particulate matter emitted by a cold engine was higher than that observed during normal engine working temperature. Received September 10, 1998. Revision March 2, 1999