Phosphoproteomics Sample Preparation Impacts Biological Interpretation of Phosphorylation Signaling Outcomes

The influence of phosphoproteomics sample preparation methods on the biological interpretation of signaling outcome is unclear. Here, we demonstrate a strong bias in phosphorylation signaling targets uncovered by comparing the phosphoproteomes generated by two commonly used methods—strong cation exchange chromatography-based phosphoproteomics (SCXPhos) and single-run high-throughput phosphoproteomics (HighPhos). Phosphoproteomes of embryonic stem cells exposed to ionizing radiation (IR) profiled by both methods achieved equivalent coverage (around 20,000 phosphosites), whereas a combined dataset significantly increased the depth (>30,000 phosphosites). While both methods reproducibly quantified a subset of shared IR-responsive phosphosites that represent DNA damage and cell-cycle-related signaling events, most IR-responsive phosphoproteins (>82%) and phosphosites (>96%) were method-specific. Both methods uncovered unique insights into phospho-signaling mediated by single (SCXPhos) versus double/multi-site (HighPhos) phosphorylation events; particularly, each method identified a distinct set of previously unreported IR-responsive kinome/phosphatome (95% disparate) directly impacting the uncovered biology.

Simultaneous Monitoring of Monoclonal Antibody Variants by Strong Cation-Exchange Chromatography Hyphenated to Mass Spectrometry to Assess Quality Attributes of Rituximab-Based Biotherapeutics

Different manufacturing processes and storage conditions of biotherapeutics can lead to a significant variability in drug products arising from chemical and enzymatic post-translational modifications (PTMs), resulting in the co-existence of a plethora of proteoforms with different physicochemical properties. To unravel the heterogeneity of these proteoforms, novel approaches employing strong cation-exchange (SCX) high-performance liquid chromatography (HPLC) hyphenated to mass spectrometry (MS) using a pH gradient of volatile salts have been developed in recent years. Here, we apply an established SCX-HPLC-MS method to characterize and compare two rituximab-based biotherapeutics, the originator MabThera® and its Indian copy product Reditux™. The study assessed molecular differences between the two drug products in terms of C-terminal lysine variants, glycosylation patterns, and other basic and acidic variants. Overall, MabThera® and Reditux™ displayed differences at the molecular level. MabThera® showed a higher degree of galactosylated and sialylated glycoforms, while Reditux™ showed increased levels of oligomannose and afucosylated glycoforms. Moreover, the two drug products showed differences in terms of basic variants such as C-terminal lysine and N-terminal truncation, present in Reditux™ but not in MabThera®. This study demonstrates the capability of this fast SCX-HPLC-MS approach to compare different drug products and simultaneously assess some of their quality attributes.

Rapid and Efficient Enrichment of Snake Venoms from Human Plasma Using a Strong Cation Exchange Tip Column to Improve Snakebite Diagnosis

Snake envenomation is a serious public health issue in many tropical and subtropical countries. Accurate diagnosis and immediate antivenom treatment are critical for effective management. However, the venom concentration in the victims’ plasma is usually low, representing one of the bottlenecks in developing clinically applicable assays for venom detection and snakebite diagnosis. In this study, we attempted to develop a simple method for rapid enrichment of venom proteins from human plasma to facilitate detection. Our experiments showed that several major protein components of both Naja atra (N. atra) and Bungarus multicinctus (B. multicinctus) venoms have higher isoelectric point (pI) values relative to high-abundance human plasma proteins and could be separated via strong cation exchange–high-performance liquid chromatography (SCX-HPLC). Based on this principle, we developed an SCX tip column-based protocol for rapid enrichment of N. atra and B. multicinctus venom proteins from human plasma. Application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) led to the identification of cytotoxin and beta-bungarotoxin as the major proteins enriched by the SCX tip column in each venom sample. The entire process of venom enrichment could be completed within 10–15 min. Combination of this method with our previously developed lateral flow strip assays (rapid test) significantly enhanced the sensitivity of the rapid test, mainly via depletion of the plasma protein background, as well as increase in venom protein concentration. Notably, the SCX tip column-based enrichment method has the potential to efficiently enrich other Elapidae snake venoms containing proteins with higher pI values, thereby facilitating venom detection with other assays. This simple and rapid sample preparation method should aid in improving the clinical utility of diagnostic assays for snakebite.

Effects of Resin Chemistries on the Selective Removal of Industrially Relevant Metal Ions Using Wafer-Enhanced Electrodeionization

Wafer-enhanced electrodeionization (WE-EDI) is an electrically driven separations technology that occurs under the influence of an applied electric field and heavily depends on ion exchange resin chemistry. Unlike filtration processes, WE-EDI can be used to selectively remove ions even from high concentration systems. Because every excess ion transported increases the operating costs, the selective separation offered by WE-EDI can provide a more energy-efficient and cost-effective process, especially for highly concentrated salt solutions. This work reports the performance comparison of four commonly used cation exchange resins (Amberlite IR120 Na+, Amberlite IRP 69, Dowex MAC 3 H+, and Amberlite CG 50) and their influence on the current efficiency and selectivity for the removal of cations from a highly concentrated salt stream. The current efficiencies were high for all the resin types studied. Results also revealed that weak cation exchange resins favor the transport of the monovalent ion (Na+) while strong cation exchange resins either had no strong preference or preferred to transport the divalent ions (Ca2+ and Mg2+). Moreover, the strong cation exchange resins in powder form generally performed better in wafers than those in the bead form for the selective removal of divalent ions (selectivity > 1). To further understand the impact of particle size, resins in the bead form were ground into a powder. After grinding the strong cation resins displayed similar behavior (more consistent current efficiency and preference for transporting divalent ions) to the strong cation resins in powder form. This indicates the importance of resin size in the performance of wafers.

Sulfonic Acid-Functionalized SBA-15 as Strong Cation-Exchange Sorbent for Solid-Phase Extraction of Atropine and Scopolamine in Gluten-Free Grains and Flours

A novel method was developed and applied to the determination of the most representative tropane alkaloids (TAs), atropine and scopolamine, in gluten-free (GF) grains and flours by HPLC-MS/MS. Accordingly a suitable sample treatment procedure based on solid-liquid extraction (SLE) and followed by strong cation-exchange solid-phase extraction (SCX-SPE) was optimized. SBA-15 mesostructured silica functionalized with sulfonic acids was evaluated as sorbent. The proposed method was fully validated in sorghum flour showing good accuracy with recoveries in the range of 93–105%, good linearity (R2 > 0.999) and adequate precision (RSD < 20%). Low method quantification limits (MQL) were obtained (1.5 and 2.4 µg/kg for atropine and scopolamine, respectively) and no matrix effect was observed thanks to the extraction and clean-up protocol applied. The method was applied to 15 types of GF samples of pseudocereals (buckwheat, quinoa and amaranth), cereals (teff, corn and blue corn, sorghum and millet) and legumes (red and green lentil, chickpea and pea). Atropine was found above the MQL in eight of them, with values between 7 and 78 µg/kg, while scopolamine was only found in teff flour, its concentration being 28 µg/kg. The method developed is an interesting tool for determining TAs in a variety of samples of GF grains and flours.