Pyridinium-based ionic liquid matrices can improve the identification of proteins by peptide mass-fingerprint analysis with matrix-assisted laser desorption/ionization mass spectrometry

Ionic Liquid-Assisted Laser Desorption/Ionization-Mass Spectrometry: Matrices, Microextraction, and Separation

Ionic liquids (ILs) have advanced a variety of applications, including matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). ILs can be used as matrices and solvents for analyte extraction and separation prior to analysis using laser desorption/ionization-mass spectrometry (LDI-MS). Most ILs show high stability with negligible sublimation under vacuum, provide high ionization efficiency, can be used for qualitative and quantitative analyses with and without internal standards, show high reproducibility, form homogenous spots during sampling, and offer high solvation efficiency for a wide range of analytes. Ionic liquids can be used as solvents and pseudo-stationary phases for extraction and separation of a wide range of analytes, including proteins, peptides, lipids, carbohydrates, pathogenic bacteria, and small molecules. This review article summarizes the recent advances of ILs applications using MALDI-MS. The applications of ILs as matrices, solvents, and pseudo-stationary phases, are also reviewed.

Proteins in Ionic Liquids: Current Status of Experiments and Simulations

In the last two decades, while searching for interesting applications of ionic liquids as potent solvents, their solvation properties and their general impact on biomolecules, and in particular on proteins, gained interest. It turned out that ionic liquids are excellent solvents for protein refolding and crystallization. Biomolecules showed increased solubilities and stabilities, both operational and thermal, in ionic liquids, which also seem to prevent self-aggregation during solubilization. Biomolecules can be immobilized, e.g. in highly viscous ionic liquids, for particular biochemical processes and can be designed to some extent by the proper choice of the ionic liquid cations and anions, which can be characterized by the Hofmeister series.

A cool and high salt-tolerant ionic liquid matrix for preferential ionization of phosphopeptides by negative ion MALDI-MS

An optimized ILM G₃THAP/PA matrix significantly improved the detection of phosphopeptides by negative ion MALDI-MS compared with using 3-AQ/CHCA/ADP and DHB/PA matrices.

Ionic liquid matrix-based dispersive liquid-liquid microextraction for enhanced MALDI-MS analysis of phospholipids in soybean

Ionic liquid matrix (ILM) is found to be a very versatile substance for analysis of broad range of organic molecules in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) due to good solubility for a variety of analytes, formation of homogenous crystals and high vacuum stability of the matrix. In the present work, an ILM, cyno-4-hydroxycinnamic acid-butylamine (CHCAB) was employed in dispersive liquid-liquid microextraction (DLLME) as sample probe and matrix for extraction and ionization of phospholipids from food samples (soybean) prior to MALDI-MS analysis. With the employed technique, 8-125 fold improvement in signal intensity and limit of detection were achieved for the analysis of phospholipids. The best extraction efficiency of phospholipids in ILM-DLLME was obtained with 5min extraction time in presence 30mg/mL CHCAB and 1.2% NaCl using chloroform as an extracting solvent and methanol as a dispersing solvent. Further, the developed ILM-DLLME procedure has been successfully applied for the analysis of phospholipids in soybean samples in MALDI-MS.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric imaging of synthetic polymer sample spots prepared using ionic liquid matrices

RATIONALE

Polymer sample spots for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) prepared by the dried-droplet method often reveal ring formation accompanied by possible segregation of matrix and sample molecules as well as of the polymer homologs itself. Since the majority of sample spots are prepared by this simple and fast method, a matrix or sample preparation method that excludes such segregation has to be found.

METHODS

Three different ionic liquid matrices based on conventionally used aromatic compounds for MALDI-TOF MS were prepared. The formation of ionic liquids was proven by (1) H NMR spectroscopy. MALDI-Imaging mass spectrometry was applied to monitor the homogeneity.

RESULTS

Our results show a superior sample spot homogeneity using ionic liquid matrices. Spots could be sampled several times without visible differences in the mass spectra. A frequently observed loss of matrix in the mass spectrometer vacuum was not observed. The necessary laser irradiance was reduced, which resulted in less polymer fragmentation.

CONCLUSIONS

Ionic liquid matrices can be used to overcome segregation, a typical drawback of conventional MALDI dried-droplet preparations. Homogeneous sample spots are easy to prepare, stable in the MS vacuum and, thereby, improve the reproducibility of MALDI.

Ionic liquid applications in peptide chemistry: synthesis, purification and analytical characterization processes

This review aims to provide a comprehensive overview of the recent advances made in the field of ionic liquids in peptide chemistry and peptide analytics.

Impact of ionic liquids in environment and humans: An overview

Ionic liquids enclose a large number of molecular structures consisting of a cation and an anion. Their physical state and their chemical properties can be tuned by different combination of the ions and a large number of ionic liquids have already been reported. Toxicity of ionic liquids is a subject of great importance concerning their likely use as greener solvents and new materials for a broad number of potential applications. This review provides relevant toxicological data published so far about this topic and includes a large range of ionic liquids based on different cations (imidazolium, pyridinium, pyrrolidinium, quaternary ammonium, quaternary phosphonium and guanidinium) and anions (halogens-Br, Cl, bis (trifluoromethyl)sulfonylamide, tetrafluoroborate, hexafluorophosphate, dicyanamide, acesulfame and saccharin, amongst others). In general, toxicity of ionic liquids depends on both ions and the effect of the cation alkyl chain length is very pronounced although the type of anion also exerts impact on the overall toxicity.

Ionic matrix for matrix-enhanced surface-assisted laser desorption ionization mass spectrometry imaging (ME-SALDI-MSI)

Matrix-enhanced surface-assisted laser desorption ionization mass spectrometry imaging (ME-SALDI MSI) has been previously demonstrated as a viable approach to improving MS imaging sensitivity. We describe here the employment of ionic matrices to replace conventional MALDI matrices as the coating layer with the aims of reducing analyte redistribution during sample preparation and improving matrix vacuum stability during imaging. In this study, CHCA/ANI (alpha-cyano-4-hydroxycinnamic acid/aniline) was deposited atop tissue samples through sublimation to eliminate redistribution of analytes of interest on the tissue surface. The resulting film was visually homogeneous under an optical microscope. Excellent vacuum stability of the ionic matrix was quantitatively compared with the conventional matrix. The subsequently improved ionization efficiency of the analytes over traditional MALDI was demonstrated. The benefits of using the ionic matrix in MS imaging were apparent in the analysis of garlic tissue sections in the ME-SALDI MSI mode.

Use of a novel ionic liquid matrix for MALDI-MS analysis of glycopeptides and glycans out of total tryptic digests

In this study, we investigated a novel ionic liquid matrix (ILM), namely, the 1,1,3,3-tetramethylguanidinium salt of 2,4,6-trihydroxyacetophenone (THAP). This matrix[1,1,3,3-tetramethylguanidinium 2,4,6-trihydroxyacetophenone (GTHAP)] turned out to be well suited for the matrix-assisted laser desorption/ionization mass spectrometric analysis of glycopeptides and glycans, and overcame the well-known ionization suppression of carbohydrate structures in the presence of peptides. The matrix was evaluated by two different series of experiments, in each case in comparison with the crystalline THAP matrix. In the first set of experiments, mass spectra were taken from unseparated tryptic digests of three glycoproteins taken as model compounds. Even glycopeptides containing short peptide backbones and large carbohydrate moieties gave high signal intensities when using the ILM though they did not appear in the THAP spectra. In the second set of experiments, the total tryptic digests were treated with endoglycosidase PNGase F to cleave off the N-linked glycans. When using the GTHAP matrix, it was possible to detect the glycans with high intensities in the presence of the tryptic peptides, whereas glycan ionization was completely suppressed when measured with the solid matrix THAP. The extent of metastable decay of glycopeptides was reduced when using the ILM. Altogether, GTHAP proved as a useful ILM particularly being superior to solid matrices in the context of glycosylation analysis.

Aniline/alpha-cyano-4-hydroxycinnamic acid is a highly versatile ionic liquid for matrix-assisted laser desorption/ionization mass spectrometry

The performance of a matrix-assisted laser desorption/ionization (MALDI) ionic liquid matrix (ILM) consisting of alpha-cyano-4-hydroxycinnamic acid (CHCA) and aniline (ANI) was evaluated to assess whether it could offer possible advantages over conventional matrices. Ultraviolet (UV), Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) and laser desorption/ionization mass spectrometry (LDI-MS) experiments were carried out with the aim of confirming the structure of the ANI-CHCA ILM. Different model analytes such as amino acids, peptides, proteins, lipids, phospholipids, synthetic polymers, and sugars were tested. Mass spectra with similar or improved signal-to-noise (S/N) ratio (compared to CHCA) were invariably obtained demonstrating the potential of this ILM as a general purpose matrix. Furthermore, protein identification by peptide mass fingerprinting (PMF) and database search was facilitated compared to CHCA since higher scores and increased sequence coverage were observed. Finally, a complex lipid mixture (i.e. a raw extract of a milk sample) analysed by MALDI-MS showed improved S/N ratio, a reduced chemical noise and a limited formation of matrix-clusters.

Ionic liquids in analytical chemistry

The role of ionic liquids (ILs) in analytical chemistry is increasing substantially every year. A decade ago there were but a handful of papers in this area of research that were considered curiosities at best. Today, those publications are recognized as seminal articles that gave rise to one of the most rapidly expanding areas of research in chemical analysis. In this review, we briefly highlight early work involving ILs and discuss the most recent advances in separations, mass spectrometry, spectroscopy, and electroanalytical chemistry. Many of the most important advances in these fields depend on the development of new, often unique ILs and multifunctional ILs. A better understanding of the chemical and physical properties of ILs is also essential.

Liquid injection field desorption/ionization-mass spectrometry of ionic liquids

Ten ionic liquids based on four types of organic cations, C(+) (imidazolium, pyrrolidinium, pyridinium, and phosphonium), combined with various types of anions, A-, were analyzed by liquid injection field desorption/ionization- (LIFDI) mass spectrometry. For the purpose of LIFDI analysis the ionic liquids were dissolved in methanol, acetonitrile or tetrahydrofuran at concentrations of 0.01-0.1 microl mL(-1). The measurements were performed on a double-focusing magnetic sector instrument. In all ionic liquid LIFDI spectra, the intact cation of the compound yielded the base peak accompanied by cluster ions of the general formula [C(2)A](+) and occasionally [C(3)A(2)](+). Tandem mass spectrometry and reconstructed ion chromatograms were employed to reveal the identity of the observed ions. Although limited to positive-ion mode, LIFDI also provided analytical information on the anions due to cluster ion formation. Depending on actual emitter condition and ionic liquid the limit of detection in survey scans was determined to 5-50 pg of ionic liquid.

Synthesis and characterization of fluorinated phosphonium ionic liquids

A wide variety of phosphonium ionic liquids containing fluorous ponytails Rfn (Rfn = –(CF2)n–1CF3; n = 4, 6, 10) are synthesized by the reaction of Rfn-(CH2)2-I with trialkylphosphines (R3P; R = Me, nBu, nOct). The efficacy of multiple metathetical routes to anion exchange have been investigated, thus the corresponding BF4–, PF6–, tosylate (OTs–) and triflate (OTf–) derivatives have also been prepared. All compounds have been comprehensively characterized by multinuclear NMR spectroscopy, ESI-MS, DSC, and TGA/SDTA, and in the case of [Me3PCH2CH2Rf4][I] by single crystal X-ray diffraction. These materials range from high melting solids (e.g., [Me3P(CH2)2Rf4][I] Tm = 195 °C) to very low melting liquids (e.g., [nOct3P(CH2)2Rf4][OTf] Tg = –64 °C), and they all have high thermal decomposition points (295 to 394 °C). Incorporation of the more weakly coordinating BF4– and PF6– yielded a significant increase in the melting point of the materials, in contrast to OTf– and OTs– derivatives, which all exhibited significantly depressed melting points.Key words: phosphonium ionic liquids, alternative solvents, fluorine, phosphorus, fluorous ponytails.

Expression of proteins with dimethylarginines in Escherichia coli for protein-protein interaction studies

Protein arginine methylation often modulates protein-protein interactions. To isolate a sufficient quantity of proteins enriched in methyl arginine(s) from natural sources for biochemical studies is laborious and difficult. We describe here an expression system that produces recombinant proteins that are enriched in omega-N(G),N(G)-asymmetry dimethylarginines. A yeast type I arginine methyltransferase gene (HMT1) is put on a plasmid under the control of the Escherichia coli methionine aminopeptidase promoter for constitutive expression. The protein targeted for post-translational modification is put on the same plasmid behind a T7 promoter for inducible expression of His(6)-tagged proteins. Sbp1p and Stm1p were used as model proteins to examine this expression system. The 13 arginines within the arginine-glycine-rich motif of Sbp1p and the RGG sequence near the C terminus of Stm1p were methylated. Unexpectedly, the arginine residue on the thrombin cleavage site (LVPRGS) of the fusion proteins can also be methylated by Hmt1p. Sbp1p and Sbp1p/hmt1 were covalently attached to solid supports for the isolation of interacting proteins. The results indicate that arginine methylation on Sbp1p exerts both positive and negative effects on protein-protein interaction.

Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives

A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxycinnamic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed.

Ionic liquid matrices with phosphoric acid as matrix additive for the facilitated analysis of phosphopeptides by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool for the analysis and characterization of protein phosphorylation on the peptide level. In this study, the applicability of ionic liquid matrices (ILM) formed by combination of the crystalline MALDI matrix 2,5-dihydroxybenzoic acid (DHB) with pyridine or n-butylamine was tested for the analysis of phosphopeptides. Low ionization efficiency in both positive and negative ion mode was observed in acid-free sample preparations. Upon addition of 0.1% trifluoroacetic acid (TFA), ion formation was increased, but analogously to the situation described earlier for pure DHB, best results were obtained upon use of 1% phosphoric acid as matrix additive. The samples prepared in this way were significantly more homogeneous than preparations with pure DHB, thus avoiding the need for time-consuming search for hot spots. Other characteristics like metastable fragmentation of phosphopeptides did not differ from that observed in classical preparations. The limits of detection for synthetic phosphopeptides and singly or multiply phosphorylated peptides from tryptic digests of alpha- and beta-casein were comparable with those obtained when using pure DHB; in some cases even higher signal intensities could be observed in the ILM. The use of ILM in combination with 1% phosphoric acid as matrix additive significantly facilitates analysis of phosphopeptides by MALDI-MS.