Protein phosphorylation stoichiometry by simultaneous ICP-QMS determination of phosphorus and sulfur oxide ions: A multivariate optimization of plasma operating conditions

Analysis of sulfur in soil and plant digests using methane as a reaction gas for ICP-MS

Quantitation of sulfur (S) is vitally important for analysis of agricultural soil and plant samples due to the requirement of S in living organisms. Although inductively coupled plasma mass spectrometry (ICP-MS) is a commonly used and robust instrument for multi-elemental detection, S is usually analysed by ICP-optical emission spectroscopy (OES) since S quantitation poses a particular challenge for ICP-MS due to interferences on all S isotopes. The requirement for analysis by two instruments increases time and cost for sample analysis, hence analysis by one instrument is desirable. The use of reaction gases in ICP-MS can improve the performance by shifting S to a mass for detection where no interference is present. This work explored the potential of methane as a reaction gas for analysis of S in soil and plant samples to give users an alternative option to oxygen. The product ion clusters CH2SH+ were monitored (m/z 47 and 49 on ICP-MS and with mass shift of +15 from Q1 → Q2 using 32 → 47 and 34 → 49 on triple quadrupole ICP-MS). As expected, triple quadrupole ICP-MS performed better than single quadrupole ICP-MS containing a reaction cell due to the ability to preselect the m/z of choice and remove ions that may react with methane in the reaction cell. The method detection limit (MDL) was 150 mg kg-1 S for plants and 53 mg kg-1 S for soils which is fit for requirements. This is the first-time methane has been reported as a reaction gas for analysis of S and shows promising results for agricultural samples when using a triple quadrupole ICP-MS. Results compared well to those obtained via the more commonly used ICP-optical emission spectroscopy (OES) method with results <20 % for all samples. Interlaboratory comparison samples were within 2 Z-scores of the consensus mean. In the absence of ICP-MS/MS, Q-ICP-MS with detection of cluster m/z 47 was deemed to be suitable for detection of S in plant samples, with acceptable MDL (250 mg kg-1 S), acceptable precision (<20 % RSD) and <20 % variation to the reported ICP-OES result.

Post translational modifications of milk proteins in geographically diverse goat breeds

Goat milk is a source of nutrition in difficult areas and has lesser allerginicity than cow milk. It is leading in the area for nutraceutical formulation and drug development using goat mammary gland as a bioreactor. Post translational modifications of a protein regulate protein function, biological activity, stabilization and interactions. The protein variants of goat milk from 10 breeds were studied for the post translational modifications by combining highly sensitive 2DE and Q-Exactive LC-MS/MS. Here we observed high levels of post translational modifications in 201 peptides of 120 goat milk proteins. The phosphosites observed for CSN2, CSN1S1, CSN1S2, CSN3 were 11P, 13P, 17P and 6P, respectively in 105 casein phosphopeptides. Whey proteins BLG and LALBA showed 19 and 4 phosphosites respectively. Post translational modification was observed in 45 low abundant non-casein milk proteins mainly associated with signal transduction, immune system, developmental biology and metabolism pathways. P_asp is reported for the first time in 47 sites. The rare conserved peptide sequence of (SSSEE) was observed in αS1 and αS2 casein. The functional roles of identified phosphopeptides included anti-microbial, DPP-IV inhibitory, anti-inflammatory and ACE inhibitory. This is first report from tropics, investigating post translational modifications in casein and non-casein goat milk proteins and studies their interactions.

A method for analyzing the composition of viral nucleoprotein complexes, produced by heterologous expression in bacteria

Viral genomes are protected and organized by virally encoded packaging proteins. Heterologous production of these proteins often results in formation of particles resembling the authentic viral capsid or nucleocapsid, with cellular nucleic acids packaged in place of the viral genome. Quantifying the total protein and nucleic acid content of particle preparations is a recurrent biochemical problem. We describe a method for resolving this problem, developed when characterizing particles resembling the Menangle Virus nucleocapsid. The protein content was quantified using the biuret assay, which is largely independent of amino acid composition. Bound nucleic acids were quantified by determining the phosphorus content, using inductively coupled plasma mass spectrometry. Estimates for the amount of RNA packaged within the particles were consistent with the structurally-characterized packaging mechanism. For a bacterially-produced nucleoprotein complex, phosphorus usually provides a unique elemental marker of bound nucleic acids, hence this method of analysis should be routinely applicable.

Determination of ultra-trace sulfur in high-purity metals by isotope dilution inductively coupled plasma sector field mass spectrometry combined with chemical separation procedure

The analytical method of ultra-trace sulfur (S) in high-purity metal by isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) combined with chemical separation procedure was developed in the present study. In order to determine the ultra-trace S in high-purity metal, a chemical separation with alumina column was carried out before ICP-MS measurement. This method enabled to prevent the polyatomic ion interference arising from the metal matrix and the signal suppression derived from the space charge effect in ICP-MS. In order to achieve high sensitive analysis, an ICP-sector field mass spectrometer (ICP-SFMS) was used. The isolation of polyatomic ion interference with respect to S was also carried out in medium-resolution mode. In addition, measurement conditions including detector dead time, which affects the precision and accuracy of the isotope dilution method, and washout conditions that were employed to reduce memory effects were optimized. The developed method was validated by the determination of S in a high-purity iron reference material (JSS-001-4). The analytical result obtained by the developed method (1.86 mg kg^-1 ± 0.12 mg kg^-1 (k = 2)) was in good agreement with the certified value (1.90 mg kg^-1 ± 0.42 mg kg^-1). The method was also applied to the determination of S in high-purity zinc, revealing a content of 0.08 mg kg^-1 ± 0.08 mg kg^-1 (k = 2). Since the developed method enabled the determination of ultra-trace S at μg kg^-1 level in the high-purity zinc, it is expected to be useful for high sensitive and accurate determination of ultra-trace S in high-purity metals.

Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments

Mass spectrometry (MS) has emerged as a tool that can analyze nearly all classes of molecules, with its scope rapidly expanding in the areas of post-translational modifications, MS instrumentation, and many others. Yet integration of novel analyte preparatory and purification methods with existing or novel mass spectrometers can introduce new challenges for MS sensitivity. The mechanisms that govern detection by MS are particularly complex and interdependent, including ionization efficiency, ion suppression, and transmission. Performance of both off-line and MS methods can be optimized separately or, when appropriate, simultaneously through statistical designs, broadly referred to as "design of experiments" (DOE). The following review provides a tutorial-like guide into the selection of DOE for MS experiments, the practices for modeling and optimization of response variables, and the available software tools that support DOE implementation in any laboratory. This review comes 3 years after the latest DOE review (Hibbert DB, 2012), which provided a comprehensive overview on the types of designs available and their statistical construction. Since that time, new classes of DOE, such as the definitive screening design, have emerged and new calls have been made for mass spectrometrists to adopt the practice. Rather than exhaustively cover all possible designs, we have highlighted the three most practical DOE classes available to mass spectrometrists. This review further differentiates itself by providing expert recommendations for experimental setup and defining DOE entirely in the context of three case-studies that highlight the utility of different designs to achieve different goals. A step-by-step tutorial is also provided.

The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides

RATIONALE

The phosphorylation of proteins is one of the most important post-translational modifications in nature. Knowledge of the quantity or degree of protein phosphorylation in biological samples is extremely important. A combination of liquid chromatography (LC) and inductively coupled plasma mass spectrometry (ICP-MS) allows the absolute and relative quantification of the phosphorus signal.

METHODS

A comparison between dynamic reaction cell quadrupole ICP-MS (DRC-Q-ICP-MS) and high-resolution sector field ICP-MS (SF-ICP-MS) in detecting signals of phosphorus-containing species using identical capillary LC (reversed-phase technology) and nebulizer settings was performed.

RESULTS

A method to diminish the reversed-phase gradient-related signal instability in phosphorus detection with LC/ICP-MS applications was developed. Bis(4-nitrophenyl)phosphate (BNPP) was used as a standard to compare signal-to-noise ratios and limits of detection (LODs) between the two instrumental setups. The LOD reaches a value of 0.8 µg L(-1) when applying the DRC technology in Q-ICP-MS and an LOD of 0.09 µg L(-1) was found with the SF-ICP-MS setup. This BNPP standard was further used to compare the absolute quantification possibilities of phosphopeptides in these two setups.

CONCLUSIONS

This one-to-one comparison of two interference-reducing ICP-MS instruments demonstrates that absolute quantification of individual LC-separated phosphopeptides is possible. However, based on the LOD values, SF-ICP-MS has a higher sensitivity in detecting phosphorus signals and thus is preferred in phosphopeptide analysis.

Monitoring of phosphorus oxide ion for analytical speciation of phosphite and phosphate in transgenic plants by high-performance liquid chromatography-inductively coupled plasma mass spectrometry

Large amounts of phosphate fertilizers utilized in agriculture and their relatively poor efficiency are of high ecological and economic concern. Therefore, transgenic plants capable of metabolizing phosphite are being engineered. In support of this biotechnological task, analytical speciation of phosphorus in biological tissues is required. In this study, plant extracts were analyzed by liquid chromatography-inductively coupled plasma mass spectrometry at m/z of elemental phosphorus and phosphorus oxide ions. Using polymeric-based anion exchange column and millimolar concentration of nitric acid in potassium phthalate mobile phase (pH 2.5), phosphite and phosphate ions were baseline resolved with retention times 6.95 ± 0.03 and 7.90 ± 0.03 min and with a total chromatographic run time 10 min. The detection limits were 1.58 and 1.74 μg P L(-1) at m/z 47, as compared to 2.18 and 2.04 μg P L(-1) at m/z 31, respectively. The results obtained in real world samples for the two detection modes were in good agreement, yet signal acquisition at m/z 47 enabled better precision without collision/reaction cell (RSD below 2%) as compared to RSD around 4% obtained at m/z 31 using He-pressurized cell (3.5 mL min(-1)).

Farm animal milk proteomics

Milk is one of the most important nutrients for humans during lifetime. Farm animal milk in all its products like cheese and other fermentation and transformation products is a widespread nutrient for the entire life of humans. Proteins are key molecules of the milk functional component repertoire and their investigation represents a major challenge. Proteins in milk, such as caseins, contribute to the formation of micelles that are different from species to species in dimension and casein-type composition; they are an integral part of the MFGM (Milk Fat Globule Membrane) that has being exhaustively studied in recent years. Milk proteins can act as enzymes or have an antimicrobial activity; they could act as hormones and, last but not least, they have a latent physiological activity encoded in their primary structure that turns active when the protein is cleaved by fermentation or digestion processes. In this review we report the last progress in proteomics, peptidomics and bioinformatics. These new approaches allow us to better characterize the milk proteome of farm animal species, to highlight specific PTMs, the peptidomic profile and even to predict the potential nutraceutical properties of the analyzed proteins.