Enhanced Universal Quantification of Biomolecules Using Element MS and Generic Standards: Application to Intact Protein and Phosphoprotein Determination

Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives

The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.

Multielement Detection of Nonmetals by Barium-Based Post-ICP Chemical Ionization Coupled to Orbitrap-MS

Prevalence of F, Cl, S, P, Br, and I in pharmaceuticals and environmental contaminants has promoted standard-free quantitation using analyte-independent heteroatom responses in inductively coupled plasma (ICP)-MS. However, in-plasma ionization challenges and element-dependent isobaric interference removal methods have hampered the multielement nonmetal detection in ICP-MS. Here, we examine an alternative approach to enhance multielement detection capabilities. Analytes are introduced into an ICP leading to post-plasma formation of HF, HCl, H3PO3, H2SO4, HBr, and HI, which are then chemically ionized to BaF+, BaCl+, BaH2PO3+, BaHSO4+, BaBr+, and BaI+ via reactions with barium-containing ions supplied by a nanospray. Subsequent ion detection by high-resolution MS provides an element-independent approach for resolving isobaric interferences. We show that elemental response factors using these ions are linear within 2 orders of magnitude and independent of analytes' chemical structures. Using a single set of operating parameters, detection limits <1 ng/mL are obtained for Cl, Br, I, and P, while those for F and S are 1.8 and 6.2 ng/mL, respectively, offering improved multielement quantitation of nonmetals. Further, insights into ionization mechanisms indicate that the reactivities of reagent ions follow the order BaNO2+ > BaHCO2+ > Ba(H2O)n2+ ∼ BaCH3CO2+. Notably, the least reactive ions are generated directly by nanospray, suggesting that modification of these ions via interaction with plasma afterglow is critical for achieving good sensitivities. Moreover, our experiments indicate that the element-specific plasma products follow the order HF < H2SO4 ∼ HCl < H3PO3 ∼ HBr ∼ HI for their propensity to react with reagent ions. These insights provide guidelines to manage matrix effects and offer pathways to further improve the technique.

AF4-UV/VIS-MALS-ICPMS/MS for the characterization of the different nanoparticulated species present in oligonucleotide-gold nanoparticle conjugates

In-depth characterization of functionalized nanomaterials is still a remaining challenge in nanobioanalytical chemistry. In this work, we propose the online coupling of Asymmetric Flow Field-Flow Fractionation (AF4) with UV/Vis, Multiangle Light Scattering (MALS) and Inductively Coupled Plasma-Tandem Mass Spectrometry (ICP-MS/MS) detectors to carry out, in less than 10 min and directly in the functionalization reaction mixture, the complete characterization of gold nanoparticles (AuNPs) functionalized with oligonucleotides and surface-modified with polyethylene glycol (PEG). AF4 separation provided full separation of the bioconjugates from the original AuNPs while P/Au and S/Au ICP-MS/MS ratios in the bioconjugate fractographic peaks could be used to compute the corresponding stoichiometries, oligonucleotide/AuNP and PEG/AuNPs. MALS detection clearly showed the coexistence of two distinct nanoparticulated populations in the bioconjugation mixture, which were demonstrated to be different not only in size but in functionality as well. The major bioconjugate population showed lower hydrodynamic ratios (18 nm) with higher and steadier oligonucleotides/AuNPs (92) and PEG/AuNPs (2350) stoichiometries, in comparison to the minor abundant population (54 nm, 51 and 1877, respectively). Moreover, the ratio between the absorbance signals measured at 520 nm and 650 nm reflects a lower AuNP aggregation in the major (10.5) than in the minor (4.5) population. Results obtained prove the benefits of a detailed characterization to find out if subsequent purification of functionalized AuNP-oligonucleotides is required to design more efficiently their final bioanalytical application.

Certification of protein biomarker standards using element MS and generic standards: Application to human cytokines

The availability of protein standards and methods for their characterization, quantification, and purity assessment are currently a bottleneck in absolute quantitative proteomics. In this work, we introduce an absolute quantitative analytical strategy based on ICP-MS sulfur detection that uses sulfate as generic standard to quantify and certify the mass purity of protein standards. The methodology combines capillary chromatographic separation with parallel detection with ICP-MS and ESI-MS to determine proteoforms concentration and identity, respectively. The workability of the methodology was demonstrated using recombinant human cytokine standards IP-10 and Flt3L (2 batches), which are relevant biomarkers for carcinoma or inflammatory diseases. Every key factor (transport efficiency, column recovery, signal stability and internal standard suitability) was taken into account and certified BSA standard was used as quality control for validation purposes. Protein quantification values and resulting mass purity certification of IP-10 and one batch of Flt3L were very high (100 and 86%, respectively). Lower mass purity obtained for another batch of Flt3L (<70%) concurred with the finding of significant proteoforms resulted from oxidation processes as observed by parallel ESI-MS.

High-Resolution Elemental Mass Spectrometry Using LC-ICP-Nanospray-Orbitrap for Simultaneous and Species-Independent Quantitation of Fluorinated and Chlorinated Compounds

Simultaneous elemental detection of F and Cl offers quantitation of fluorinated and chlorinated compounds and their transformation products without compound-specific standards. Despite wide-ranging applications, this capability has been hindered by fundamental and technical shortcomings of current inductively coupled plasma (ICP)-MS methods in ion formation and isobaric interference elimination. These hurdles are alleviated here via a chemical ionization method. Fluorine and chlorine in analytes are first converted to HF and HCl by an ICP with post-plasma recombination and subsequently react with barium-containing ions supplied by a nanospray, yielding BaF+ and BaCl+ as elemental reporter ions. Notably, the method is readily interfaced to an Orbitrap MS which eliminates isobaric interferences at resolving powers as low as 35,000, far greater than that of current ICP-MS instruments. Moreover, the instrument is easily reverted to the ESI-MS mode for complementary molecular characterization. To demonstrate analytical capabilities, a workflow for rapid quantitation of compounds separated by reversed-phase liquid chromatography is developed using a species-independent calibration. The independent F and Cl measurements agree with each other, providing recoveries of >90% and LODs of 8-12 pmol Cl and 5-12 pmol F on the column. The workflow along with LC-ESI-MS on the same instrument is then applied to identify and quantify in-vitro drug metabolites, yielding total drug-related material recoveries of >80% and quantitation of minor metabolites summing to 8% of the total drug-related compounds. These results highlight the strengths of simultaneous F and Cl speciation for rapid quantitation with applications in early drug development.

Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani

We report a novel hybrid, molecular and elemental mass spectrometry (MS) setup for the absolute quantification of snake venom proteomes shown here for two desert black cobra species within the genus Walterinnesia, Walterinnesia aegyptia and Walterinnesia morgani. The experimental design includes the decomplexation of the venom samples by reverse-phase chromatography independently coupled to four mass spectrometry systems: the combined bottom-up and top-down molecular MS for protein identification and a parallel reverse-phase microbore high-performance liquid chromatograph (RP-μHPLC) on-line to inductively coupled plasma (ICP-MS/MS) elemental mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously record the absolute sulfur concentration throughout the chromatogram and assign it to the parent venom proteins separated in the RP-μHPLC-ESI-QToF parallel run via mass profiling. The results provide a locus-resolved and quantitative insight into the three desert black cobra venom proteome samples. They also validate the units of measure of our snake venomics strategy for the relative quantification of snake venom proteomes as % of total venom peptide bonds as a proxy for the % by weight of the venom toxins/toxin families. In a more general context, our work may pave the way for broader applications of hybrid elemental/molecular MS setups in diverse areas of proteomics.

Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance

Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.

Calibration-Free Single-Molecule Absolute Quantification Using Super-resolution Microscopy

Single-molecule (SM) quantification has become a powerful analytical technique in the fields of physics, chemistry, and biology. SM imaging, especially with super-resolution (SR) techniques, has dramatically facilitated the study of individual molecules that may function as disease-related biomarkers. Although multiple properties can be used for quantitative imaging analysis, counting may be the simplest and most direct way. Consequently, how to utilize the greater spatial resolution to overcome undercounting or overcounting errors in certain conditions shows promising potential to unravel intracellular mechanisms of isolated biomolecules. From this perspective, we present an absolute quantification approach, termed crucial connected-component entropy (CCCE), with subresolution accuracy for the SR SM detection platform without the need for prior knowledge of calibration, and a cross-validation analytical pipeline based on SM profiling for nanoscale performance assessments. Considering its high efficiency, accuracy, and robustness for routine SM quantification compared with commonly used strategies, we believe that this protocol will indubitably find wide applications in biochemistry research, drug discovery, and clinical diagnostics, especially molecular diagnostics.