Is proton cationization promoted by polyatomic primary ion bombardment during time-of-flight secondary ion mass spectrometry analysis of frozen aqueous solutions?

Ion bombardment of pure water ice by Au+ monoatomic and Au3 + and C60 + polyatomic projectiles results in the emission of two series of water cluster ions-(H2O)n + and (H2O)nH+-with n ranging from 1 to >40. The cluster ion yields are very significantly higher under polyatomic ion bombardment than when using an Au+ primary ion. The yield of the protonated water species (H2O)nH+ is found to be enhanced by increasing ion fluence. C60 + bombardment results in a very dramatic increase in the (H2O)nH+ yield and decrease in the yield of (H2O)n +. Au3 + also significantly increased the yield of protonated species relative to the non-protonated but to a lesser extent than C60 +. Bombardment by Au+ also increased the yield of protonated species but to a very much smaller extent. The hypothesis that the protonated species may enhance the yield of [M+H]+ from solute molecules in solution has been investigated using two amino acids, alanine and arginine, and a nucleic base, adenine. The data suggest that the protons produced by the sputtering of water ice are depleted in the presence of these solutes and concurrently the yields of solute-related [M+H]+ and immonium secondary ions are greatly enhanced. These yield enhancements are analysed in the light of other possible contributors such as increased rates of sputtering under polyatomic beams and increased secondary ion yields as a consequence of solute dispersion. It is concluded that enhanced proton attachment is occurring in polyatomic sputtered frozen aqueous solutions.     

Peak assignment in multi-capillary column–ion mobility spectrometry using comparative studies with gas chromatography–mass spectrometry for VOC analysis

Over the past years, ion mobility spectrometry (IMS) as a well established method within the fields of military and security has gained more and more interest for biological and medical applications. This highly sensitive and rapid separation technique was crucially enhanced by a multi-capillary column (MCC), pre-separation for complex samples. In order to unambiguously identify compounds in a complex sample, like breath, by IMS, a reference database is mandatory. To obtain a first set of reference data, 16 selected volatile organic substances were examined by MCC-IMS and comparatively analyzed by the standard technique for breath research, thermal desorption–gas chromatography–mass spectrometry. Experimentally determined MCC and GC retention times of these 16 compounds were aligned and their relation was expressed in a mathematical function. Using this function, a prognosis of the GC retention time can be given very precisely according to a recorded MCC retention time and vice versa. Thus, unknown MCC-IMS peaks from biological samples can be assigned—after alignment via the estimated GC retention time—to analytes identified by GC/MS from equivalent accomplished data. One example of applying the peak assignment strategy to a real breath sample is shown in detail.     

Summary of ISO/TC 201 Standard: ISO 22415—Surface chemical analysis—Secondary ion mass spectrometry—Method for determining yield volume in argon cluster sputter depth profiling of organic materials

The International Standard ISO 22415 provides methods to measure sputtering yield volumes of organic test materials using argon cluster ions. The test materials should consist of thin films of known thicknesses between 50 and 1000 nm. The format of the test materials, the measurement of sputtering ion dose, sputtered depth, and reporting requirements for sputtering yield volumes are described.     

Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis?

Formalin‐fixed and paraffin‐embedded (FFPE)–tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE‐treatment provides excellent conservation of the three‐dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous nonspecific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE‐tissue by fit‐for‐purpose proteomics technologies. We demonstrate that many protein modifications and cross‐links remain after treatment and conclude that the proteomics of FFPE‐tissue is of value, but clear‐cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low‐level proteins and/or biologically relevant modifications is seriously hampered by the FFPE‐treatment. Peptide assignment should only be performed on high‐quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: “Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.”     

Semi‐quantitative non‐target analysis of water with liquid chromatography/high‐resolution mass spectrometry: How far are we?

Combining high‐resolution mass spectrometry (HRMS) with liquid chromatography (LC) has considerably increased the capability of analytical chemistry. Among others, it has stimulated the growth of the non‐target analysis, which aims at identifying compounds without their preceding selection. This approach is already widely applied in various fields, such as metabolomics, proteomics, etc. The applicability of LC/HRMS‐based non‐target analysis in environmental analyses, such as water studies, would be beneficial for understanding the environmental fate of polar pollutants and evaluating the health risks exposed by the new emerging contaminants. During the last five to seven years the use of LC/HRMS‐based non‐target analysis has grown rapidly. However, routine non‐target analysis is still uncommon for most environmental monitoring agencies and environmental scientists. The main reasons are the complicated data processing and the inability to provide quantitative information about identified compounds. The latter shortcoming follows from the lack of standard substances, considered so far as the soul of each quantitative analysis for the newly discovered pollutants. To overcome this, non‐target analyses could be combined with semi‐quantitation. This Perspective aims at describing the current methods for non‐target analysis, the possibilities and challenges of standard substance‐free semi‐quantitative analysis, and proposes tools to join these two fields together.     

High‐resolution mass spectrometry for bioanalytical applications: Is this the new gold standard?

Liquid chromatography coupled to quadrupole‐based tandem mass spectrometry (QqQ) is termed the “gold standard” for bioanalytical applications because of its unpreceded selectivity, sensitivity, and the ruggedness of the technology. More recently, however, high‐resolution mass spectrometry (HRMS) has become increasingly popular for bioanalytical applications. Nonetheless, this technique is still viewed, either as a screening technology or as a research tool. Although HRMS is actively discussed during scientific conferences, it is yet to be widely utilised in routine laboratory settings and there remains a reluctance to use HRMS for quantitative measurements in regulated environments. This paper does not aim to comprehensively describe the potential of the latest HRMS technology, but rather, it focuses on what results can be obtained and outlines the author's experiences over a period of many years of the routine application of various forms of HRMS instrumentation. Fifteen years ago, some nine different QqQ methods were used in the author's laboratory to analyse a variety of different veterinary drug resides. Today, many more analytes are quantified by seven HRMS methods and just three QqQ methods remain in use for the analysis of a small set of compounds yet to be upgraded to HRMS analysis. This continual upgrading and migration of analytical methods were accompanied by regularly participating in laboratory proficiency tests (PTs). The PT reports (covering a range of analytes and analytical methods) were used to compare the accuracy of HRMS‐ versus QqQ‐based measurements. In the second part of this paper, the particular strengths and limitations of HRMS for both method development and routine measurements are critically discussed. This also includes some anecdotal experiences encountered when replacing QqQ assays with HRMS methods.     

Versatile lipid profiling by liquid chromatography–high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer

Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC–HRMS or LC–MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC–HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and “all ion fragmentation” (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale.     

Are AM1 ligand‐protein binding enthalpies good enough for use in the rational design of new drugs?

We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation (e.g., MP2 or B3LYP). Species studied include alkanes, aromatic systems, molecules including groups with hypervalent sulfur or with donor or acceptor hydrogen bonding capability, as well as ammonium or carboxylate ions. B3LYP/6-311+G(2d,p) binding energies correlated very well with the BSSE corrected MP2/6-31G(d) values. AM1 binding enthalpies also showed good correlation with MP2 values, and their systematic deviation is acceptable when enthalpies are used for the comparison of interaction energies between ligands and a target. PM3 otherwise gave erratic energy differences in comparison to the B3LYP or MP2 approaches. As one would expect, the geometries of the binding complexes showed the known limitations of the semiempirical and DFT methods. AM1 calculations were subsequently applied to a test set consisting of "real" protein active site-ligand complexes. Preliminary results indicate that AM1 could be a valuable tool for the design of new drugs using proteins as templates. This approach also has a reasonable computational cost. The ligand-protein X-ray structures were reasonably reproduced by AM1 calculations and the corresponding AM1 binding enthalpies are in agreement with the results from the "small molecules" test set.     

Comprehensive profiling of <Emphasis Type="Italic">N</Emphasis>-acylhomoserine lactones produced by <Emphasis Type="Italic">Yersinia pseudotuberculosis</Emphasis> using liquid chromatography coupled to hybrid quadrupole–linear ion trap mass spectrometry

A method for the comprehensive profiling of the N-acylhomoserine lactone (AHL) family of bacterial quorum-sensing molecules is presented using liquid chromatography (LC) coupled to hybrid quadrupole–linear ion trap (QqQLIT) mass spectrometry. Information-dependent acquisition (IDA), using triggered combinations of triple-quadrupole and linear ion trap modes in the same LC-MS/MS run, was used to simultaneously screen, quantify and identify multiple AHLs in a single sample. This MS method uses common AHL fragment ions attributed to the homoserine moiety and the 3-oxo-, 3-hydroxy- or unsubstituted acyl side chains, to identify unknown AHLs in cell-free culture supernatants in an unbiased manner. This LC-MS technique was applied to determine the relative molar ratios of AHLs produced by Yersinia pseudotuberculosis and the consequences of inactivating by mutation either or both of the AHL synthase genes (ypsI and ytbI) on AHL profile and concentration. The Y. pseudotuberculosis wild type but not the ypsI ytbI double mutant produced at least 24 different AHLs with acyl chains ranging from C4 to C15 with or without 3-oxo or 3-hydroxy substituents. YtbI, in contrast to YpsI, could direct the synthesis of all of the AHLs identified. The most abundant and hence most biologically relevant Y. pseudotuberculosis AHLs were found to be the 3-oxo-substituted C6, C7 and C8 AHLs and the unsubstituted C6 and C8 compounds. The LC-QqQLIT methodology is broadly applicable to quorum-sensing signal molecule analysis and can provide comprehensive AHL profiles and concentrations from a single sample and simultaneously collect confirmatory spectra for each AHL identified. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Catharine A. Ortori and Steve Atkinson made an equal contribution to the paper.     

Modeling hydrogen evolution from the Fe4S4 and Fe8S9X (X = N,C) clusters. Can a Fe?S high‐spin cluster serve as a surrogate for the FeMo cofactor?

A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.