Why are nH-perfluoroalkanoate ions more mobile than expected? Implications for identifying an emerging environmental pollutant.

nH-Perfluoroalkyl carboxylic acids (nH-PFCAs) are emerging pollutants. Their identification by ion mobility is frustrated by the nH-PFCAs having unexpectedly small collision cross sections (CCS). Theory and experiment agree that this is because nH-PFCA ions undergo internal hydrogen bridging, and this insight will help guide the creation of more accurate methods for pollutant identification.

Estimation of thermodynamic and physicochemical properties of the alkali astatides: On the bond strength of molecular astatine (At2 ) and the hydration enthalpy of astatide (At- ).

The recent accurate and precise determination of the electron affinity (EA) of the astatine atom At0 warrants a re-investigation of the estimated thermodynamic properties of At0 and astatine containing molecules as this EA was found to be much lower (by 0.4 eV) than previous estimated values. In this contribution we estimate, from available data sources, the following thermodynamic and physicochemical properties of the alkali astatides (MAt, M = Li, Na, K, Rb, Cs): their solid and gaseous heats of formation, lattice and gas-phase binding enthalpies, sublimation energies and melting temperatures. Gas-phase charge-transfer dissociation energies for the alkali astatides (the energy requirement for M+ At- ➔ M0 + At0 ) have been obtained and are compared with those for the other alkali halides. Use of Born-Haber cycles together with the new AE (At0 ) value allows the re-evaluation of ΔHf (At0 )g (=56 ± 5 kJ/mol); it is concluded that (At2 )g is a weakly bonded species (bond strength <50 kJ/mol), significantly weaker bonded than previously estimated (116 kJ/mol) and much weaker bonded than I2 (148 kJ/mol), but in agreement with the finding from theory that spin-orbit coupling considerably reduces the bond strength in At2 . The hydration enthalpy (ΔHaq ) of At- is estimated to be -230 ± 2 kJ/mol (using ΔHaq [H+ ] = -1150.1 kJ/mol), in good agreement with molecular dynamics calculations. Arguments are presented that the largest alkali halide, CsAt, like the smallest, LiF, will be only sparingly soluble in water, following the generalization from hard/soft acid/base principles that "small likes small" and "large likes large."

Increased Targeting Area in Tumors by Dual-Ligand Modification of Liposomes with RGD and TAT Peptides.

Modification with polyethylene glycol (PEGylation) and the use of rigid phospholipids drastically improve the pharmacokinetics of chemotherapeutics and result in more manageable or reduced side-effects. A major drawback is retarded cellular delivery of content, which, along with tumor heterogeneity, are the two main obstacles against tumor targeting. To enhance cellular delivery and reach a bigger area of a tumor, we designed liposomes decorated with two ligands: one for targeting tumor vasculature via a cyclic-pentapeptide containing arginine-glycine-aspartic acid (RGD), which impacts tumor independent of passive accumulation inside tumors, and one for extravascular targeting of tumor cells via a cell-penetrating peptide derived from human immunodeficiency virus type 1 transactivator of transcription (TAT). Liposomes with different ligand combinations were prepared and compared with respect to performance in targeting. Intravital imaging illustrates the heterogeneous behavior of RGD-liposomes in both intravascular and extravascular distribution, whereas TAT-liposomes exhibit a predictable extravascular localization but no intravascular targeting. Dual-ligand modification results in enhanced vascular targeting and a predictable extravascular behavior that improves the therapeutic efficacy of doxorubicin-loaded liposomes but also an augmented clearance rate of liposomes. However, the dual-modified liposome could be a great candidate for targeted delivery of non-toxic payloads or contrast agents for therapeutic or diagnostic purposes. Here we show that the combination of vascular-specific and tumor cell-specific ligands in a liposomal system is beneficial in bypassing the heterogeneous expression of tumor-specific markers.

Lipid signature of advanced human carotid atherosclerosis assessed by mass spectrometry imaging.

Carotid atherosclerosis is a risk factor for ischemic stroke, one of the main causes of mortality and disability worldwide. The disease is characterized by plaques, heterogeneous deposits of lipids, and necrotic debris in the vascular wall, which grow gradually and may remain asymptomatic for decades. However, at some point a plaque can evolve to a high-risk plaque phenotype, which may trigger a cerebrovascular event. Lipids play a key role in the development and progression of atherosclerosis, but the nature of their involvement is not fully understood. Using matrix-assisted laser desorption/ionization mass spectrometry imaging, we visualized the distribution of approximately 200 different lipid signals, originating of >90 uniquely assigned species, in 106 tissue sections of 12 human carotid atherosclerotic plaques. We performed unsupervised classification of the mass spectrometry dataset, as well as a histology-directed multivariate analysis. These data allowed us to extract the spatial lipid patterns associated with morphological plaque features in advanced plaques from a symptomatic population, revealing spatial lipid patterns in atherosclerosis and their relation to histological tissue type. The abundances of sphingomyelin and oxidized cholesteryl ester species were elevated specifically in necrotic intima areas, whereas diacylglycerols and triacylglycerols were spatially correlated to areas containing the coagulation protein fibrin. These results demonstrate a clear colocalization between plaque features and specific lipid classes, as well as individual lipid species in high-risk atherosclerotic plaques.

Down-Regulation of Collagen Hydroxylation in Colorectal Liver Metastasis.

Collagen is significantly upregulated in colorectal liver metastasis (CRLM) compared to liver tissue. Expression levels of specific collagen types in CRLM resemble those in colorectal cancer (CRC) and colon tissue. We investigated whether the collagen hydroxylation pattern from the primary tumor also migrates with the metastatic tumor. The degree of collagen alpha-1(I) hydroxylation in colon, CRC, liver, and CRLM tissue of the same individuals (n = 14) was studied with mass spectrometry. The degree of hydroxylation was investigated in 36 collagen alpha-1(I) peptides, covering 54% of the triple helical region. The degree of hydroxylation in liver tissue was similar to that in colon tissue. The overall degree of hydroxylation was significantly lower (9 ± 14%) in CRC tissue and also significantly lower (12 ± 22%) in CRLM tissue compared to colon. Furthermore, eleven peptides with a specific number of hydroxylations are significantly different between CRLM and liver tissue; these peptides could be candidates for the detection of CRLM. For one of these eleven peptides, a matching naturally occurring peptide in urine has been identified as being significantly different between patients suffering from CRLM and healthy controls. The hydroxylation pattern in CRLM resembles partly the pattern in liver, primary colorectal cancer and colon.

A mono-acyl phospholipid (20:1 lyso-PS) activates Toll-Like Receptor 2/6 hetero-dimer.

Toll-like receptor 2 (TLR2) is an important pattern recognition receptor on the surface of host immune cells that binds a variety of ligands that are released by microorganisms as well as by damaged or dying host cells. According to the current concept, TLR2/1 and TLR2/6 heterodimers are activated by tri- or di-acylated ligands, respectively. However, also mono-acyl phospholipid containing lipid fractions derived from parasites, were reported to be able to activate TLR2. In order to provide conclusive evidence for the TLR2 activating capacity of mono-acyl phospholipids derived from pathogens, we developed a biosynthetic method to enzymatically convert commercially available phospholipids into several mono-acyl-phospholipid variants that were examined for their TLR2 activating capacity. These investigations demonstrated that 1-(11Z-eicosenoyl)-glycero-3-phosphoserine 20:1 (20:1 lyso-PS) is a true agonist of the TLR2/6 heterodimer and that its polar headgroup as well as the length of the acyl chain are crucial for TLR2 activation. In silico modelling further confirmed 20:1 mono-acyl PS as a ligand for TLR2/6 heterodimer, as this predicted that multiple hydrogen bonds are formed between the polar headgroup of 20:1 mono-acyl PS and amino acid residues of both TLR2 and TLR6. Future studies can now be performed to further assess the functions of 20:1 lyso-PS as an immunological mediator, because this enzymatic method enables its preparation in larger quantities than is possible by isolation from the parasite that naturally produces this compound, Schistosoma mansoni, the source of the original discovery (Van der Kleij et al., 2002).

Metabolic changes related to the IDH1 mutation in gliomas preserve TCA-cycle activity: An investigation at the protein level.

The discovery of the IDH1 R132H (IDH1 mut) mutation in low-grade glioma and the associated change in function of the IDH1 enzyme has increased the interest in glioma metabolism. In an earlier study, we found that changes in expression of genes involved in the aerobic glycolysis and the TCA cycle are associated with IDH1 mut. Here, we apply proteomics to FFPE samples of diffuse gliomas with or without IDH1 mutations, to map changes in protein levels associated with this mutation. We observed significant changes in the enzyme abundance associated with aerobic glycolysis, glutamate metabolism, and the TCA cycle in IDH1 mut gliomas. Specifically, the enzymes involved in the metabolism of glutamate, lactate, and enzymes involved in the conversion of α-ketoglutarate were increased in IDH1 mut gliomas. In addition, the bicarbonate transporter (SLC4A4) was increased in IDH1 mut gliomas, supporting the idea that a mechanism preventing intracellular acidification is active. We also found that enzymes that convert proline, valine, leucine, and isoleucine into glutamate were increased in IDH1 mut glioma. We conclude that in IDH1 mut glioma metabolism is rewired (increased input of lactate and glutamate) to preserve TCA-cycle activity in IDH1 mut gliomas.

Collagen analysis with mass spectrometry.

Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.

One electron less or one proton more: how do they differ?

From the NIST website and the literature, we have collected the Ionisation Energies (IE) of 3,052 and the Proton Affinities (PA) of 1,670 compounds. For 614 of these, both the IE and PA are known; this enables a study of the relationships between these quantities for a wide variety of molecules. From the IE and PA values, the hydrogen atom affinities (HA) of molecular ions M•+ may also be assessed. The PA may be equated to the heterolytic bond energy of [MH]+ and HA to the homolytic bond energy. Plots of PA versus IE for these substances show (in agreement with earlier studies) that, for many families of molecules, the slope of the ensuing line is less negative than -1, i.e. changes in the PA are significantly less than the concomitant opposite changes in IE. At one extreme (high PA, low IE) are the metals, their oxides and hydroxides, which show a slope of close to -1, at the other extreme (low PA, high IE) are the hydrogen halides, methyl halides and noble gases, which show a slope of ca. -0.3; other molecular categories show intermediate behaviour. One consequence of a slope less negative than -1 is that the changes in ionic enthalpies of the protonated species more closely follow the changes in the enthalpies of the neutral molecules compared with changes in the ion enthalpies of the corresponding radical cations. This is consistent with findings from ab initio calculations from the literature that the incoming proton, once attached to the molecule, may retain a significant amount of its charge. These collected data allow a comparison of the thermodynamic stability of protonated molecules in terms of their homolytic or heterolytic bond cleavages. Protonated nitriles are particularly stable by virtue of the very large hydrogen atom affinities of their radical cations.

Data Processing Pipeline for Lipid Profiling of Carotid Atherosclerotic Plaque with Mass Spectrometry Imaging.

Atherosclerosis is a lipid and inflammation-driven disease of the arteries that is characterized by gradual buildup of plaques in the vascular wall. A so-called vulnerable plaque, consisting of a lipid-rich necrotic core contained by a thin fibrous cap, may rupture and trigger thrombus formation, which can lead to ischemia in the heart (heart attack) or in the brain (stroke). In this study, we present a protocol to investigate the lipid composition of advanced human carotid plaques using matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI), providing a framework that should enable the discrimination of vulnerable from stable plaques based on lipid composition. We optimized the tissue preparation and imaging methods by systematically analyzing data from three specimens: two human carotid endarterectomy samples (advanced plaque) and one autopsy sample (early stage plaque). We show a robust data reduction method and evaluate the variability of the endarterectomy samples. We found diacylglycerols to be more abundant in a thrombotic area compared to other plaque areas and could distinguish advanced plaque from early stage plaque based on cholesteryl ester composition. We plan to use this systematic approach to analyze a larger dataset of carotid atherosclerotic plaques.

Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry.

Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 41 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 45 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, that is, 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).

Neoantigens in Chronic Obstructive Pulmonary Disease and Lung Cancer: A Point of View.

The goal of this manuscript is to explore the role of clinical proteomics for detecting mutations in chronic obstructive pulmonary disease (COPD) and lung cancer by mass spectrometry-based technology. COPD and lung cancer caused by smoke inhalation are most likely linked by challenging the immune system via partly shared pathways. Genome-wide association studies have identified several single nucleotide polymorphisms which predispose an increased susceptibility to COPD and lung cancer. In lung cancer, this leads to coding mutations in the affected tissues, development of neoantigens, and different functionality and abundance of proteins in specific pathways. If a similar reasoning can also be applied in COPD will be discussed. The technology of mass spectrometry has developed into an advanced technology for proteome research detecting mutated peptides or proteins and finding relevant molecular mechanisms that will enable predicting the response to immunotherapy in COPD and lung cancer patients.

Tissue proteomics outlines AGR2 AND LOX5 as markers for biochemical recurrence of prostate cancer.

Although many patients are cured from prostate cancer (PCa) by surgery only, there are still patients who will experience rising prostate-specific antigen (PSA) levels after surgery, a condition known as biochemical recurrence (BCR). Novel protein prognostic markers in PCa tissue might enable finding better treatment for those patients experiencing BCR with a high chance of metastasis. In this study, we aimed to identify altered proteins in prostate cancer tissue, and to evaluate their potential role as prognostic markers. We used two proteomics strategies to analyse 34 prostate tumours (PCa) and 33 normal adjacent prostate (NAP) tissues. An independent cohort of 481 samples was used to evaluate the expression of three proteins: AGR2, FASN and LOX5 as prognostic markers of the disease. Tissue microarray immunohistochemical staining indicated that a low percentage of positive tumour cells for AGR2 (HR (95% CI) = 0.61 (0.43-0.93)), and a low percentage of positive tumour cells for LOX5 expression (HR (95% CI) = 2.53 (1.23-5.22)) are predictors of BCR after RP. In contrast, FASN expression had no prognostic value for PCa.

Proton affinities and ion enthalpies.

Proton affinities of a number of alkyl acetates (CH3-C(=O)-OR) and of methyl alkanoates (R-C(=O)-OCH3, R=H, alkyl) have been assembled from the literature or measured using the kinetic method. It was observed that the proton affinities for the isomeric species CH3-C(=O)-OR and R-C(=O)-OCH3 are almost identical, an unexpected result as the charge in these protonated ester molecules is largely at the keto carbon atom and so this site should be more sensitive to alkyl substitution. Analysis of the data, including those from lone pair ionisation and core-electron ionisation experiments available from the literature, indicate that after protonation, extensive charge relaxation (or polarisation) takes place (as is also the case, according to the literature, after core-electron ionisation). By contrast, after lone pair ionisation, which results in radical cations, such relaxation processes are relatively less extensive. As a consequence, changes in ion enthalpies of these protonated molecules follow more closely the changes in neutral enthalpies, compared with changes in enthalpies of the corresponding radical cations, formed by electron detachment. Preliminary analyses of published energetic data indicate that the above finding for organic esters may well be another example of a more general phenomenon.

Metal ion hydrocarbon bidentate bonding in alkyl acetates, methyl alkanoates, alcohols and 1-alkenes: a comparative study.

The relative affinity of the monovalent metal ions Li+, Na+, Cu+ and Ag+ towards a series of aliphatic alkyl acetates and some selected 1-alkenes (P) was examined using the kinetic method. A detailed analysis of the dissociation characteristics of a series of mixed metal-bound dimer ions of the type P1-M+-P2 and the evaluated proton affinities (PAs) of the monomers shows that the affinity of the cation towards long-chain alkyl acetates and alkenes (having a chain length ≤ C4) is markedly enhanced. In line with recent studies of nitriles, alcohols and methyl alkanoates, this is attributed to a bidentate interaction of the metal ion with the functional group or double bond and the aliphatic chain. In particular, the longer chain alkyl acetates, methyl alkanoates and alcohols show a remarkably similar behaviour with respect to silver ion hydrocarbon bonding. The Ag+ adducts of the alkyl acetates dissociate by loss of CH3COOH. This reaction becomes more pronounced at longer chain lengths, which points to metal ion bidentate formation in [Ag+···1-alkene] product ions having a long hydrocarbon chain. In the same vein, the heterodimers [1- hexene···Ag+···1-heptene] and [1- heptene···Ag+···1-octene] dissociate primarily into [Ag+···1-heptene] and [Ag+···1-octene] ions, respectively. Hydrocarbon bidentate formation in [Ag+···1-octene] also reveals itself by the reluctance of this ion to react with water in an ion trap, as opposed to [Ag+···1-hexene] which readily undergoes hydration.

Interaction of metal cations with functionalised hydrocarbons in the gas phase: further experimental evidence for solvation of metal ions by the hydrocarbon chain.

Relative affinity measurements of monovalent metal ions (= Li(+), Cu(+) and Ag(+)) towards aliphatic amines, alcohols and methyl alkanoates (P) have been performed using the kinetic method on the dissociation of metal bound dimer ions of the type P(1)-M(+)-P(2). It was found that the cations' affinity towards long chain (≥C(4) chain length) n- and s-alkylamines, n-alkanols and methyl n- alkanoates was unexpectedly enhanced. This is attributed to a bidentate interaction of the metal ion with the amine, alcohol or ester functional group and the aliphatic chain, paralleling earlier observations on metal bound nitriles. Methyl substitution at the functional group (s-alkylamines compared with n-alkylamines) serves to strengthen only the N•••M(+) bond, and this can be rationalized by the larger proton affinities of s-alkylamines compared to n-alkylamines. This substitution, however, has no effect on the metal ion-hydrocarbon bond. In contrast, methyl substitution remote from the functional group, as in iso-pentylamine, does lead to strengthening of the metal ion-hydrocarbon bond. The cuprous ion affinity of hexadecylamine, C(16)H(33)NH(2) was found to be as large as that for ethylenediamine (352 kJ mol(-1)), known to be a strong copper binding agent. It is argued that such a metal ion-hydrocarbon interaction does not occur in the metal bound dimers.

Evaluation of different pretreatment protocols to detect accurately clinical carbapenemase-producing Enterobacteriaceae by MALDI-TOF.

OBJECTIVES: Carbapenemase-resistant bacteria are increasingly spreading worldwide causing public concern due to their ability to elude antimicrobial treatment. Early identification of these bacteria is therefore of high importance. Here, we describe the development of a simple and robust protocol for the detection of carbapenemase activity in clinical isolates of Enterobacteriaceae, suitable for routine and clinical applications. METHODS: The final protocol involves cellular lysis and enzyme extraction from a defined amount of bacterial cells followed by the addition of a benchmark drug (e.g. the carbapenem antibiotic imipenem or ertapenem). Carbapenem inactivation is mediated by enzymatic hydrolysis (cleavage) of the ß-lactam common structural motif, which can be detected using MALDI-TOF MS. RESULTS: A total of 260 strains were studied (208 carbapenemase producers and 52 non-carbapenemase producers) resulting in 100% sensitivity and 100% specificity for the KPC, NDM and OXA-48-like PCR-confirmed positive isolates using imipenem as benchmark. Differences between the benchmark (indicator) antibiotics imipenem and ertapenem, buffer constituents and sample preparation methods have been investigated. Carbapenemase activity was further characterized by performing specific inhibitor experiments. Intraday and interday reproducibility (coefficient of variation) of the observed hydrolysis results were 15% and 30%, respectively. A comparative study of our extraction method and a recently published method using whole bacterial cells is presented and differences are discussed. CONCLUSIONS: Using this method, an existing carbapenemase activity can be directly read from the mass spectrum as a ratio of hydrolysed product and substrate, setting an important step towards routine application in clinical laboratories.

Interaction of metal cations with alkylnitriles in the gas phase: solvation of metal ions by the hydrocarbon chain.

Relative affinity measurements of monovalent metal ions (M = Li(+), Na(+), Cu(+)and Ag(+)) toward aliphatic nitriles have been performed using the kinetic method by dissociation of metal bound dimer ions of the type R1C≡N-M(+)-N≡CR(2). It is found, particularly for Cu(+) and Ag(+), that the affinity towards nitriles having long chains (>C(6)) is markedly enhanced. This is attributed to a bidentate interaction of the metal ion with the nitrile moiety and the aliphatic chain. Theoretical calculations on the copper complexes show that these bidentate structures enjoy about 30% greater copper ion affinities compared to their linear counterparts. Such aliphatic interactions also play a major role in the dissociation chemistry of copper bound tetramers of the kind (RC≡N)(4)Cu(2+∙) where the long aliphatic chain R curls around the copper ion to facilitate electron transfer or a redox reaction to produce (RC≡N)(2)Cu(+) + RC≡N(+∙) + RC≡N.

Dimerization of peptides by calcium ions: investigation of a calcium-binding motif.

We investigated calcium-binding motifs of peptides and their recognition of active functionalities for coordination. This investigation generates the fundamentals to design carrier material for calcium-bound peptide-peptide interactions. Interactions of different peptides with active calcium domains were investigated. Evaluation of selectivity was performed by electrospray ionization mass spectrometry by infusing solutions containing two different peptides (P1 and P2) in the presence of calcium ions. In addition to signals for monomer species, intense dimer signals are observed for the heterodimer ions (P1 ⋯ Ca(2+) ⋯ P2) (⋯ represents the noncovalent binding of calcium with the peptide) in the positive ion mode and for ions ([P1-2H](2-) ⋯ Ca(2+) ⋯ [P2-2H](2-)) in the negative ion mode. Monitoring of the dissociation from these mass selected dimer ions via the kinetic method provides information on the calcium affinity order of different peptide sequences.

Identifying Ca2+-binding sites in proteins by liquid chromatography-mass spectrometry using Ca2+-directed dissociations.

Here we describe a new method to identify calcium-binding sites in proteins using high-resolution liquid chromatography-mass spectrometry in concert with calcium-directed collision-induced dissociations. Our method does not require any modifications to the liquid chromatography-mass spectrometry apparatus, uses standard digestion protocols, and can be applied to existing high-resolution MS data files. In contrast to NMR, our method is applicable to very small amounts of complex protein mixtures (femtomole level). Calcium-bound peptides can be identified using three criteria: (1) the calculated exact mass of the calcium containing peptide; (2) specific dissociations of the calcium-containing peptide from threonine and serine residues; and (3) the very similar retention times of the calcium-containing peptide and the free peptide.