Proposal for a common nomenclature for fragment ions in mass spectra of lipids.

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

Ionic dynamics mediate spontaneous termination of seizures and postictal depression state.

Epileptic seizures are characterized by periods of recurrent, highly synchronized activity that spontaneously terminates, followed by postictal state when neuronal activity is generally depressed. The mechanisms for spontaneous seizure termination and postictal depression remain poorly understood. Using a realistic computational model, we demonstrate that termination of seizure and postictal depression state may be mediated by dynamics of the intracellular and extracellular ion concentrations. Spontaneous termination was linked to progressive increase of intracellular sodium concentration mediated by activation of sodium channels during highly active epileptic state. In contrast, an increase of intracellular chloride concentration extended seizure duration making possible long-lasting epileptic activity characterized by multiple transitions between tonic and clonic states. After seizure termination, the extracellular potassium was reduced below baseline, resulting in postictal depression. Our study suggests that the coupled dynamics of sodium, potassium, and chloride ions play a critical role in the development and termination of seizures. Findings from this study could help identify novel therapeutics for seizure disorder.

Ambient suspended particulate matter and ionic speciation in Asian countries during 1998-2007.

Atmospheric acid precursor emissions in Asia are increasing at a significant rate. This is expected to continue for the next several years. This main purpose for this study is to observe the concentration variations of PM(2.5), PM(2.5-10), PM(10), total suspended particulates (TSP), atmospheric particulates, and dry deposition fluxes of ionic species in Asian countries during the years 1998-2007. The results show that the average ionic species concentration order for chloride ions (Cl(-)) in PM(10) was China > Taiwan > Korea. The average ionic species concentration order for nitrate ions (NO(3)(-)) species in PM(10) was China > Taiwan > Korea for Asian countries. In addition, the average ionic species sulfate ion (SO(4)(2-)) concentrations in PM(10) were 13.248 and 18.497 (µg/m(3)) in Taiwan and China, respectively, during the years 1998-2006. However, the average ionic species concentrations order for ammonium ions (NH(4)(+)) in PM(10) was Taiwan > China > Korea the years 2000-2006. Moreover, the average ionic species concentration order for chloride ions (Cl(-)) in PM(2.5) was Japan > Taiwan > Korea > China in the years 1998-2006. And the average ionic species concentration order for nitrate ions (NO(3)(-)) in PM(2.5) was Korea > China > Japan > Taiwan for Asian countries during 1998-2006. Moreover, the average ionic species concentration order for sulfate ions (SO(4)(2-)) in PM(2.5) was China > Korea > Taiwan > Japan in the years 1998-2006. As for the average ionic species concentration order for ammonium ion (NH(4)(+)) in PM(2.5), China > Taiwan > Japan > Korea in the years 1999-2006. Finally, the mean ionic species of nitrate ions (NO(3)(-)), sulfate ions (SO(4)(2-)) and ammonium ions (NH4(+)) were found highest in China compared with the rest of the other Asian countries during the years 1998-2006.

Influence of size on apparent scrambling of sequence during CID of b-type ions.

We investigated the influence of peptide size on the apparent loss of sequence during collision-induced dissociation (CID) of b ions using a group of peptides containing from between 4 and 10 residues. Although scrambling of sequence for b3+ generated from tetrapeptides is minimal, significant formation of nondirect sequence ions (i.e., ions for which scrambling has apparently occurred) was observed for all larger b ions included in the study.

Prediction of the doubly charged ion pattern by modelling the high- and low-resolution mass spectra of isotopomeric forms.

The presence of doubly charged ions in mass spectra is detected only occasionally because their clusters are observed more rarely than singly charged ones. The patterns connected with doubly charged ions are located in the spectrum below M/2. The narrow shapes of such patterns as well as overlapping with other bands generate significant problems in their interpretation. The method described here is based on modelling of the isotopomeric form of single- and double-charged mass ion clusters. The present work attempts to explain the generation of the double charge disotopomeric patterns of high- as well as low-resolution spectra. Predicting the high-resolution mass cluster is simpler than calculations of the low-resolution cluster. The high-resolution cluster may represent the initial form of low-resolution pattern formation.

Detection of symmetrical decomposition of molecules--isotopomeric analysis of the M/2 clusters.

The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this area many perturbations may be observed. The coincidence of different fragmentation pathways, the existence of multiply charged ions, background levels, etc. can all contribute to this problem. The present paper reports the application of multi-isotopomeric analysis methods for low-resolution ms. We present a solution that may be useful for detection of the symmetrical decomposition of a molecule and for elucidation of cluster ion genesis. The complex character of the cluster does not perturb determination of the contents of the investigated pattern. In such cases the dominated component is applied in subsequent computations.

Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry.

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) is the best MS technology for obtaining exact mass measurements owing to its great resolution and accuracy, and several outstanding FT-ICR/MS-based metabolomics approaches have been reported. A reliable annotation scheme is needed to deal with direct-infusion FT-ICR/MS metabolic profiling. Correlation analyses can help us not only uncover relations between the ions but also annotate the ions originated from identical metabolites (metabolite derivative ions). In the present study, we propose a procedure for metabolite annotation on direct-infusion FT-ICR/MS by taking into consideration the classification of metabolite-derived ions using correlation analyses. Integrated analysis based on information of isotope relations, fragmentation patterns by MS/MS analysis, co-occurring metabolites, and database searches (KNApSAcK and KEGG) can make it possible to annotate ions as metabolites and estimate cellular conditions based on metabolite composition. A total of 220 detected ions were classified into 174 metabolite derivative groups and 72 ions were assigned to candidate metabolites in the present work. Finally, metabolic profiling has been able to distinguish between the growth stages with the aid of PCA. The constructed model using PLS regression for OD(600) values as a function of metabolic profiles is very useful for identifying to what degree the ions contribute to the growth stages. Ten phospholipids which largely influence the constructed model are highly abundant in the cells. Our analyses reveal that global modification of those phospholipids occurs as E. coli enters the stationary phase. Thus, the integrated approach involving correlation analyses, metabolic profiling, and database searching is efficient for high-throughput metabolomics.

Hydrochemical analysis and evaluation of groundwater quality in Tumkur Taluk, Karnataka state, India.

Tumkur Taluk is located in the southeastern corner of Karnataka state between 13 degrees 06'30'' to 13 degrees 31' 00'' North latitude and 76 degrees 59' 00'' to 77 degrees 19' 00'' East Longitude. The Taluk spreads over an area of 1043 sq.km falling within the semiarid region and frequently facing water scarcity as well as quality problems. The major sources of employment are agriculture, horticulture and animal husbandry, engaging almost 80% of the workforce. Water samples are collected from 269 stations during pre-monsoon and 279 locations during post-monsoon of the year 2006, and were subjected to analysis for chemical characteristics. The type of water that predominates in the study area is Ca-Mg-HCO3 type during both pre- and post-monsoon seasons of the year 2006, based on hydro-chemical facies. Besides, suitability of water for irrigation is evaluated based on sodium adsorption ratio, residual sodium carbonate, sodium percent, salinity hazard and USSL diagram.

A collision cross-section database of singly-charged peptide ions.

A database of ion-neutral collision cross-sections for singly-charged peptide ions is presented. The peptides included in the database were generated by enzymatic digestion of known proteins using three different enzymes, resulting in peptides that differ in terms of amino acid composition as well as N-terminal and C-terminal residues. The ion-neutral collision cross-sections were measured using ion mobility (IM) spectrometry that is directly coupled to a time-of-flight (TOF) mass spectrometer. The ions were formed by a matrix-assisted laser desorption ionization (MALDI) ion source operated at pressures (He bath gas) of 2 to 3 torr. The majority (63%) of the peptide ion collision cross-sections correlate well with structures that are best described as charge-solvated globules, but a significant number of the peptide ions exhibit collision cross-sections that are significantly larger or smaller than the average, globular mobility-mass correlation. Of the peptide ions having larger than average collision cross-sections, approximately 71% are derived from trypsin digestion (C-terminal Arg or Lys residues) and most of the peptide ions that have smaller (than globular) collision cross-sections are derived from pepsin digestion (90%).

Modeling of isotopomeric cluster of the molecular ion.

The occurrence of poly-isotopic elements in a molecule or ion can result in complex isotopomeric cluster of an ion. The "isotopomer" better and correctly indicates different isotopic compositions of a molecule (compound) or ion and not a single atom. The ions of organic compounds show in accurate mass spectra single, isolated peaks or narrow sub-clusters regardless of their molecular masses. The occurrence of a PIE makes the molecular ion cluster more complex and significantly influences the location of the most abundant peak and the form of the cluster. The present study is an attempt at answering the following question: what is the mechanism of the molecular ion's isotopomeric cluster formation and is it step-by-step predictable? The accurate mass-resolved isotopomer cluster can be predicted from accurate masses and abundances of the stable isotopes. The cluster consists of several sub-patterns, each of which is composed of near signals (at the same nominal m/z). The range of the sub-cluster usually does not exceed 0.005 u. The low-resolution cluster can be predicted from the high-resolution pattern by addition of all peaks occurring over a given narrow mass range (m/z - 0.5; m/z+0.49). Surprisingly, predicting the accurate mass cluster is simpler than predicting the low-resolution one. A compliance of the model results with the experimental ones suggests a correct prediction.

Model calculations of the spontaneous curvature, mean and Gaussian bending constants for a thermodynamically open surfactant film.

The spontaneous curvature (H(0)), mean and Gaussian bending constants (k(c) and k (c)), as defined in the well-known Helfrich expression, have been calculated from a detailed model for a thermodynamically open surfactant layer. The effect of head group cross-section area, surfactant tail length and electrolyte concentration for monovalent ionic surfactants have been investigated. Geometrical packing constraints subjected to the aggregated hydrocarbon tails and electrostatics are found to be the dominant contributions to H(0), k(c) and k (c). In addition, the transition from spherocylindrical micelles to vesicles were investigated in terms of the three parameters and the following simple expressions were derived as criteria for coexistence between micelles and vesicles H(0)=1/4 xi and N(ves)/N(mic)=exp[4 pi(k(c)+k (c))/kT], where xi is the thickness of the hydrocarbon part of the film and N(mic) and N(ves) the average aggregation numbers of micelles and vesicles, respectively. However, it is found that the ratio N(ves)/N(mic) is order of magnitudes too large for vesicles to form at all in charged single-surfactant systems where the surfactant head is of moderate size.