Observation of low molecular weight poly(methylsilsesquioxane)s by graphite plate laser desorption/ionization time-of-flight mass spectrometry

Silicon surface assisted laser desorption ionization mass spectrometry for quantitative analysis

The approach to quantitative analysis by silicon Surface Assisted Laser Desorption Ionization Mass Spectrometry (Si-SALDI) is proposed. The approach is based on the new method for forming an active surface layer on a silicon substrate by exposing to laser radiation directly in the ion source of a mass spectrometer. The method can be used repeatedly on the same substrate, providing high reproducibility of its surface ionization properties and high ionization efficiency of organic compounds. Within the proposed approach, the methods of improvement of signal reproducibility are also considered, including continuous monitoring of the silicon surface ionization properties using a Knudsen effusion cell; scanning the surface of a silicon substrate with a laser beam; selecting the optimal value of laser fluence and using a reproducible sample introduction technique. It is demonstrated that this approach can be successfully applied to quantify clinically relevant concentrations of pharmaceutical drugs in extracts of blood.

A study of the application of graphite MALDI to the analysis of short-chain polyethylene glycols

MALDI-MS using colloidal graphite matrix doped with lithium chloride for the successful analysis of low molecular weight polymers.

Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomics

The use of offline liquid chromatography-matrix assisted laser desorption/ionization (LC-MALDI) tandem mass spectrometry (MS/MS) for bottom-up proteomics offers advantages in terms of cost, ease of use, and the time-decoupled nature of the separation step and the mass analysis. A method was developed to improve the capabilities of LC-MALDI-MS/MS in terms of protein identification in a bottom-up proteomic workflow. Enhanced protein identification is achieved by an increase in the MALDI signal intensity of the precursor peptides brought about by coating the MALDI plate with a thin film of graphite powder. Using the Escherichia coli proteome, it is demonstrated that the graphite-modified MALDI plates used in an offline LC-MALDI-MS/MS bottom-up protocol led to a 50-135% increase in the number of peptide identifications, and a concomitant 21%-105% increase in the number of proteins inferred. We identify factors that lead to improvements in peptide sequence identifications and in the number of unique proteins identified when compared to using an unmodified MALDI plate. These improvements are achieved using a low cost approach that it is easy to implement, requires no hardware/protocol modification, it is compatible with LC and adds no additional analysis time.

Benzimidazole, coumrindione and flavone derivatives as alternate UV laser desorption ionization (LDI) matrices for peptides analysis

Background

Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization mass spectrometric technique, allowing the analysis of bio-molecules and other macromolecules. The matrix molecules require certain characteristic features to serve in the laser desorption/ionization mechanism. Therefore, only a limited number of compounds have been identified as ultraviolet- laser desorption/ionization (UV-LDI) matrices. However, many of these routine matrices generate background signals that useful information is often lost in them. We have reported flavones, coumarindione and benzimidazole derivatives as alternate UV-LDI matrices.

Results

Thirty one compounds have been successfully employed by us as matrices for the analysis of low molecular weight (LMW) peptides (up to 2000 Da). Two peptides, bradykinin and renin substrate tetra-decapeptide were analyzed by using the newly developed matrices. The MS measurements were made after mixing the matrix solution with analyte by using dried droplet sample preparation procedures. The synthesized matrix materials showed better S/N ratios and minimal background signals for low mass range. Furthermore, pico molar concentrations of [Glu¹]-fibrinopeptide B human could be easily analyzed with these matrices. Finally, BSA-digest was analyzed and identified through database search against Swiss-Prot by using Mascot.

Conclusions

These results validate the good performance of the synthesized UV-laser desorption/ionization (LDI) matrices for the analysis of low molecular weight peptides.

Quantification of citrulline by parallel fragmentation monitoring--a novel method using graphitized carbon nanoparticles and MALDI-TOF/TOF mass spectrometry

BACKGROUND

Selected reaction monitoring (SRM) is a reliable mass spectrometry (MS)-based technique for quantification of small molecules. However, it is not applicable to matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem MS (MALDI-TOF/TOF MS) instruments. This work presents a novel comparable MALDI-TOF/TOF MS technique, "Parallel Fragmentation Monitoring" (PFM), for high-throughput quantification of citrulline.

METHOD

Calibrator/sample solutions were spiked with internal standard that was a stable isotopic analog with 1 mass unit heavier than citrulline. Both citrulline and internal standard were isolated and fragmented in parallel by MALDI-TOF/TOF MS in the presence of graphitized carbon nanoparticles as matrix. The ratio of the peak intensities of the selected fragment of citrulline to that of internal standard was used to calibrate/calculate the concentrations of citrulline in samples.

RESULTS

Linear calibration curves were obtained in the range of 10-250 μmol/l citrulline with correlation coefficients ≥0.997. Stored calibration curve and batch-specific calibration curve produced highly similar measurement values. Within- and between-day CVs were 3.1-8.7% and 3.5-10.6%, respectively, illustrating the reliability and robustness of PFM.

CONCLUSION

Using citrulline for proof-of-concept, we have developed the PFM technique with tremendous potential for high-throughput quantification of amino acids and other small molecules.

Graphite supported preparation (GSP) of α-cyano-4-hydroxycinnamic acid (CHCA) for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for peptides and proteins

Graphite as MALDI matrix or in combination with other substances has been reported in recent years. Here, we demonstrate that graphite can be used as target coating supporting the crystallization of the α-cyano-4-hydroxycinnamic acid matrix. A conventional dried-droplet preparation of matrix and analyte solution on a graphite-coated metal target leads to a thin, uniform layer of cubic crystals with about 1 μm edge length. Commercially available graphite powder of 1-2 μm particle size is gently wiped over the target using a cotton Q-tip, leading to an ultra-thin, not-visible film. This surface modification considerably improves analysis of peptides and proteins for MALDI MS using conventional dried-droplet preparation. Compared with untreated targets, the signal intensities of standard peptides are up to eight times higher when using the graphite supported crystallization. The relative standard deviation in peak area of angiotensin II for sample amounts between 1 and 50 fmol is reduced to about 15 % compared with 45 % for untreated sample holders. For a quantification of 1 fmol of the peptide using an internal standard the coefficient of variation is reduced to 3.5 % from 8 %. The new graphite supported preparation (GSP) protocol is very simple and does not require any technical nor manual skills. All standard solvents for peptides and proteins can be used.

Characterization and Some Insights into the Reaction Chemistry of Polymethylsilsesquioxane or Methyl Silicone Resins

Structural characterization of a polymethylsilsesquioxane (PMSQ) and a DT-type methyl silicone resin (MeDT) has been carried out by various instrumental analyses including GPC, NMR, gas chromatography, and gas chromatography-mass spectrometry. Although the PMSQ had aMwaround 5000, the resin contained a significant amount of low molecular weight species consisting of T2[MeSi(OH)O2/2] and T3[MeSiO3/2] units, ranging from to including many isomers. One isomer of was isolated of which structure was determined as a cage structure. The species are supposed to consist mainly of cyclotetra- and cyclopentasiloxanes, but presence of strained rings such as cyclotrisiloxane rings also was suggested. In MeDT, species in which the T2units in the molecules from PMSQ is replaced with D2[Me2SiO2/2] were found, for example, , suggesting that general silicone resins consist of similar structures as silsesquioxanes. The Mark-Houwink exponent for these methyl resins was~0.3, indicating the molecular shape to be compact. Investigation on the formation chemistry of the cubic octamers indicates that siloxane bond rearrangement is an important mechanism in the molecule build-up process.

Laser desorption/ionization on the layer of graphene nanoparticles coupled with mass spectrometry for characterization of polymers

A novel method for the characterization of polymers by laser desorption/ionization on the layer of graphene nanoparticles coupled with time-of-flight mass spectrometry was demonstrated. Various polymers including polypropylene glycol, polystyrene and polymethyl methacrylate with average molecular weights from 425 to 3500 Da were analyzed.

Structure and Properties of Polysilsesquioxanes and Copolymers for Ultra-Low Dielectric Films

Polysilsesquioxanes (PSSQs) with the empirical formula (RSiO3/2)n have become very important as low-dielectric insulators for copper interconnects in the next-generation logic devices, but the detailed structure-property relationships were completely lacking. We have investigated the microstructure and functional properties of PSSQs with varying alkyl substituents and also PSSQ copolymers. As a result, significant advances have been made in the scientific understanding of PSSQ structures and significant improvements of key properties such as the crack resistance, mechanical modulus and hardness, and incorporation of nanometer-sized (<4 nm) porosity for ultra-low dielectric constants (<2.0).

1H-pteridine-2,4-dione (lumazine): a new MALDI matrix for complex (phospho)lipid mixtures analysis

Nowadays, matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry represents an emerging and versatile tool for analysis of lipids. However, direct (i.e., with no previous separation of lipid classes) analysis of crude extracts containing a complex mixture of lipids (a problem typically encountered in shotgun lipidomics) is still a quite challenging task using a conventional MALDI matrix such as 2,5-dihydroxybenzoic acid (DHB). Indeed, in the presence of phospholipids containing quaternary ammonium groups, such as phosphatidylcholines and sphingomyelins, strong ionization-suppression effects are experienced especially in positive ion mode. To overcome this limitation, lumazine (1H-pteridine-2,4-dione) was evaluated as an alternative matrix. Lumazine in the solid state showed an absorption maximum at 350 nm, ionizes/desorbs without appreciable decomposition and extensive cluster formation, and can be used in both ion modes. In positive ion mode, the main species were M(*+) and 2M(*+) radical cations and cationized species ([M+H](+), [M+Na](+), [M+2Na+2Li-3H](+)). In negative ion mode, the main signals observed were the deprotonated molecular ion and the radical anion. The signal-to-noise ratio for phosphatidylglycerols and phosphatidylethanolamines using lumazine was almost 1 order of magnitude higher than that observed for DHB. Lumazine was successfully used for MALDI analysis (positive and negative ion modes) of crude lipid extracts of milk, soymilk, and hen egg, where phosphatidylethanolamines, phosphatidylserines, and phosphatidylinositols could additionally be detected.

Atmospheric pressure laser desorption/ionization of plant metabolites and plant tissue using colloidal graphite

Colloidal graphite is a promising matrix for atmospheric pressure laser desorption/ionization mass spectrometry. Intact [M+H](+) and [M-H](-) ions are readily produced from a wide range of small molecule plant metabolites, particularly anthocyanins, fatty acids, lipids, glycerides, and ceramides. Compared with a more traditional organic acid matrix, colloidal graphite provides more efficient ionization for small hydrophobic molecules and has a much cleaner background spectrum, especially in negative ion mode. Some important metabolites, e.g., fatty acids and glycosylated flavonoids, can be observed from Arabidopsis thaliana leaf and flower petal tissues in situ.

Proton sponge: a novel and versatile MALDI matrix for the analysis of metabolites using mass spectrometry

Here, we show the usefulness of a strong base, 1,8-bis(dimethyl-amino)naphthalene (DMAN; proton sponge), as a novel matrix for MALDI-TOF/MS analysis of anions. Several strong and weakly acidic low-molecular-weight analytes (fatty acids, amino acids, fatty acid-amino acid conjugates, plant and animal hormones, vitamins, and short peptides) were measured at physiologically relevant concentrations. Clear negative-mode MALDI-TOF/MS spectra of all analytes using DMAN as the matrix show only deprotonated analyte signals at a low picomole/femtomole limit-of-detection. Moreover, the spectra were totally devoid of any matrix-related signals. Standard calibration curves gave good linearity over the entire picomole range: over two concentration orders in most cases and over three orders for peptides. Using this method, the crude regurgitate of the tobacco hornworm caterpillars (Manduca sexta, Lepidoptera, Sphingidae) was analyzed. As many as 11 different components were identified from a single spot, including 16:0, 18:2, 18:3, and 21:0 free acids and 5:0-Glu, 6:0-Glu, 18:2-Glu, 18:3-Glu, 16:0-Glu, and 16:3-Glu fatty acid-amino acid conjugates (FACs) in complete qualitative agreement with previously reported anion exchange-HPLC analyses. The identity of these components was confirmed by negative ion collision-induced dissociation (CID) MS2 spectra.

Role of carbon nano-materials in the analysis of biological materials by laser desorption/ionization-mass spectrometry

At present, carbon nano-materials are being utilized in various procedures, especially in laser desorption/ionization-mass spectrometry (LDI-MS) for analyzing a range of analytes, which include peptides, proteins, metabolites, and polymers. Matrix-oriented LDI-MS techniques are very well established, with weak organic acids as energy-absorbing substances. Carbon materials, such as nano-tubes and fullerenes are being successfully applied in the small-mass range, where routine matrices have strong background signals. In addition, the role of carbon nano-materials is very well established in the fractionation and purification fields. Modified diamond powder and surfaces are utilized in binding peptides and proteins from complex biological fluids and analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). Polylysine-coated diamond is used for solid-phase extraction to pre-concentrate DNA oligonucleotides. Graphite is useful for desalting, pre-concentration, and as energy-absorbing material (matrix) in desorption/ionization. Carbon nano-tubes in their different derivatized forms are used as matrix materials for the analysis of a range of analytes, such as carbohydrates, amino acids, peptides, proteins, and some environmental samples by LDI-MS. Fullerenes are modified in different ways to bind serum entities analyzed through MALDI/TOF-MS and are subsequently utilized in their identifications. In addition, the fullerenes are a promising matrix in LDI-MS, but improvements are needed.

2B or not 2B, that is the question: further investigations into the use of pencil as a matrix for matrix-assisted laser desorption/ionisation

The effective use of pencil as a matrix for matrix-assisted laser desorption/ionisation (MALDI) for the study of actinides has previously been demonstrated (Black et al., Rapid Commun. Mass Spectrom. 2006; 20: 1053). Here, the scope of the types of molecules amenable to analysis by this method has been extended, establishing that approximately 90% of a library containing 50 diverse small molecules can be successfully analysed by this technique. Further, the role played by the bulk materials present in the different pencil leads has been investigated and a simple one-step deposition of matrix and calibration materials has been achieved through the fabrication of different calibration pencils (Cali-Pens).

Single drop microextraction as a concentrating probe for rapid screening of low molecular weight drugs from human urine in atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry

The present work reports the development of a new analytical procedure for simple and rapid screening of low molecular weight drugs (<500 Da) from human urine samples by atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) combined with single drop microextraction (SDME). The success of the proposed method is due to the use of methyltrioctylammonium chloride (MTOAC) as additive to avoid the noise arising from the matrix ions (alpha-cyano-4-hydroxycinnamic acid (CHCA)). SDME also aided in alleviating the interferences arising from other matrix ions present in the urine samples prior to AP-MALDI-MS analysis. Factors affecting the extraction efficiency of drugs, such as selection of solvent, stirring speed, extraction time, exposure volume of extraction phase and salt addition, have been optimized. The optimum molar ratio of CHCA/MTOAC that gave the minimum background noise of CHCA ions was 700:1. The limit of detection (LOD) and relative standard deviation (RSD) of the method were in the ranges 0.3-1.6 microM and 7.8-11.4%, respectively. The SDME method was compared with liquid-liquid extraction (LLE) and hollow fiber liquid-phase microextraction (HF-LPME) to evaluate the compatibility of the present method in the extraction of drugs from urine samples. The role of MTOAC as matrix ion signal suppressor and SDME as analyte-separating device in the rapid screening of low molecular weight drugs from human urine samples using AP-MALDI/MS has been reported.

Identification of carbohydrates by matrix-free material-enhanced laser desorption/ionisation mass spectrometry

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) is a sensitive mass spectrometric technique which utilises acidic materials as matrices for laser energy absorption, desorption and ionisation of analytes. These matrix materials produce background signals particularly in the low-mass range and make the detection and identification of small molecules difficult and nearly impossible. To overcome this problem this paper introduces matrix-free material-enhanced laser desorption/ionisation mass spectrometry (mf-MELDI-MS) for the screening and analysis of small molecules such as carbohydrates. For this purpose, 4,4'-azo-dianiline was immobilised on silica gel enabling the absorption of laser energy sufficient for successful desorption and ionisation of low molecular weight compounds. The particle and pore sizes, the solvent system for suspension and the sample preparation procedures have been optimised. The newly synthesised MELDI material delivered excellent spectra with regard to signal-to-noise ratio and detection sensitivity. Finally, wheat straw degradation products and Salix alba L. plant extracts were analysed proving the high performance and excellent behaviour of the introduced material.

Immobilized carbon nanotubes as matrix for MALDI-TOF-MS analysis: applications to neutral small carbohydrates

In this work, we reported on the advantages of immobilized carbon nanotubes as a novel MALDI-matrix. Recently, carbon nanotubes have been reported to be an effective MALDI matrix for small molecules (Anal. Chem.2003, 75, 6191), as it can eliminate the interfering matrix peaks as well as form a web morphology to fully disperse the analyte and allow strong ultraviolet absorption for enhanced pulsed laser desorption and ionization. In our study, to overcome the problem that the carbon nanotube matrix may fly off from the target, a type of polyurethane adhesive, NIPPOLAN-DC-205, is introduced to immobilize carbon nanotubes on the target, which enables widespread application of carbon nanotubes as matrix for MALDI-MS analysis. At the same time, the properties of the carbon nanotubes as an efficient matrix remained after immobilization. The presence of NIPPOLAN-DC-205 increases the time for analysis at a particular desorption spot by minimizing the time-consuming search for "hot spots" and facilitating experiments such as post source decay (PSD) which need longer-lasting signals. Moreover, NIPPOLAN-DC-205 produces no interference peaks and can easily be cleaned with acetone. Fast evaporation technology may be used to enhance signal reproducibility in MALDI analysis using carbon nanotubes as matrix. Consequently, the applicability of the carbon nanotube as matrix for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of low molecular mass analytes is highly improved. The feasibility of the method employing polyurethane is demonstrated by comparison of the results produced from the carbon nanotube matrix with and without immobilization. In addition, neutral small carbohydrates, which are difficult to be ionized normally, can be cationized with high efficiency by MALDI-TOF-MS using the immobilized carbon nanotube matrix. The method was further applied to analyze peptides and detect urine glucose successfully.

Carbon Nanotubes as Assisted Matrix for Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Analysis of low molecular weight compounds with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed by using carbon nanotubes obtained from coal by arc discharge as the matrix. The carbon nanotube matrix functions as substrate to trap analytes of peptides, organic compounds, and beta-cyclodextrin deposited on its surface. It has been found that carbon nanotubes can transfer energy to the analyte under laser irradiation, which makes analytes well desorbed/ionized, and the interference of intrinsic matrix ions can be eliminated. At the same time, the fragmentation of the analyte can be avoided. A good sensitivity and excellent reproducibility of the spectrum signals are achieved. It is believed that this work not only will open a new field for applications of carbon nanotubes, but also will offer a new technique for high-speed analysis of low molecular weight compounds in areas such as metabolism research and characterization of natural products.

Analysis of fatty acids by graphite plate laser desorption/ionization time-of-flight mass spectrometry

Fatty acids obtained from triglycerides (trioelin, tripalmitin), foods (milk, corn oil), and phospholipids (phosphotidylcholine, phosphotidylserine, phosphatidic acid) upon alkaline hydrolysis were observed directly without derivatization by graphite plate laser desorption/ionization time-of-flight mass spectrometry (GPLDI-TOFMS). Mass-to-charge ratios predicted for sodium adducts of expected fatty acids (e.g. palmitic, oleic, linoleic and arachidonic acids) were observed without interference. Although at present no quantitation is possible, the graphite plate method enables a simple and rapid qualitative analysis of fatty acids.