Immunoaffinity Enrichment Research Articles

A Novel High-Throughput Immunoaffinity LC-MS/MS Assay for P-III-NP and Other Fragments of Type III Procollagen in Human Serum.

The amino-terminal propeptide of type III procollagen (P-III-NP) is used with IGF-I to detect the illicit use of growth hormone and to monitor growth hormone therapy. However, the only currently available assays for P-III-NP are immunoassays, which are not well harmonized. In addition, other fragments of type III procollagen may better evaluate collagen turnover. We aimed to develop a high-throughput assay using immunoaffinity enrichment coupled to ultra-high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify peptides belonging to three different regions of type III procollagen in human serum simultaneously. To facilitate higher throughput, we transferred the assay from microcentrifuge tubes to a 96-well plate format with partially automated pipetting. The method was linear (Pearson's R ≥ 0.994) over an estimated concentration range of 1.35-13.3 nM, 0.04-2.28 nM, and 0.26-5.1 nM for each surrogate peptide of P-III-NP, collagen degradation products, and the carboxyl-terminal propeptide, respectively. Intra-day and inter-day imprecision were both < 13.6%, and the results of robustness testing were also encouraging. The method was successfully applied to capillary blood samples obtained using Tasso+ microsampling devices. Modest correlation of P-III-NP concentration was observed between our new method and a WADA-approved immunoassay (N = 40, Pearson's R = 0.789) with a significant bias of -87.8%. Our method simultaneously quantifies four peptides belonging to three regions of type III procollagen in human serum. High bias between assays highlights the need for common higher-order calibrators or reference materials to help improve the comparability of results across laboratories.

Semi-quantitative analysis of serum and cerebrospinal fluid transferrin glycoforms by top-down liquid chromatography mass spectrometry

Detection of β-2 transferrin in body fluid could help identify cerebrospinal fluid (CSF) leakage. The most common method, isoelectric focusing, was qualitative and could not provide detailed N-glycan structural information. We presented an alternative method using top-down liquid chromatography-time of flight mass spectrometry (LC-TOF MS). After immunoaffinity enrichment, fluid transferrin glycoforms were analyzed by a high-resolution LC-TOF MS, and the N-glycan structure predicted by accurate mass. The performance was validated with imprecision at 15%, with a cut-off of 0.04 for β-2 transferrin to tetrasialotransferrin ratio to confirm the presence of CSF in fluid samples.

Improving the Sensitivity of Protein Quantification by Immunoaffinity Liquid Chromatography─Triple Quadrupole Mass Spectrometry Using an Iterative Transition Summing Technique.

The desire to reach ever-diminishing lower limits of quantification (LLOQ) to probe changes in low abundance protein targets has led to enormous progress in sample preparation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) instrumentation. To maximize signal and reduce noise, many approaches have been employed, including specific immunoaffinity (IA) enrichment and reducing the LC flow to the nanoflow (nLC) level; however, additional sensitivity gains may still be required. Recently, a technique termed "echo summing" has been described for small-molecular-weight analytes on a triple quadrupole (QqQ) MS where multiple iterations of the same, single selected reaction monitoring (SRM) transition are collected, summed, and integrated, yielding significant analyte dependent signal-to-noise (S/N) improvements. Herein, the direct applicability of echo summing to protein quantification by sequential IA combined with nLC-MS/MS (IA-nLC-MS/MS) is described for a beta nerve growth factor (NGF) and a soluble asialoglycoprotein receptor (sASGPR) assay from human serum. Five iterations of echo summing outperformed traditional collection in relative average accuracy (-1.5 ± 7.7 vs -41.7 ± 10.7% bias) and precision (7.8 vs 18.4% coefficient of variation (CV)) of the low-end quality control (QC) sample (N = 4) for NGF and improved functional sensitivity of serially diluted serum QC samples (N = 5 each population) approximately 2-fold (1.96 and 2.00-fold) for two peptides of sASGPR. Echo summing also extended the minimum quantifiable QC level for sASGPR 4-fold lower. Similar gains are believed to be achievable for most protein IA-nLC-MS/MS assays.

Enhanced analysis of equine plasma for the presence of recombinant human erythropoietin - Implementation of an improved workflow.

An improved screening workflow and a robust capillary flow LC-MS confirmatory method for the detection of recombinant human erythropoietin (rHuEPO) has been implemented to increase the sensitivity of rHuEPO detection and to reduce the number of suspect samples committed to confirmatory testing. The influence of repeated dosing of epoetin-β on the detection window of rHuEPO in equine plasma was assessed using the optimised method. Samples were initially assessed using an economical R&D Human EPO Duo-Set ELISA Development System. Samples indicating a result greater than the batch baseline were analysed using the complementary R&D Human EPO Quantikine IVD ELISA kit. All samples recording an abnormal screening result were subjected to confirmatory analysis. Confirmation of rHuEPO in plasma (≥2.5ml) in the range of 4-13 mIU/ml (n = 6) was achieved using immunoaffinity enrichment, tryptic digestion, and capillary flow LC-MS/MS. Four horses were administered a single dose of epoetin-β (10,000 IU) via the subcutaneous and intravenous routes, on two occasions, seven days apart. The excretion profile was rapid with epoetin-β detection times of 48 to 72 h following each administration, with no appreciable difference observed between the two routes of administration. This workflow has been shown as an effective anti-doping strategy related to rHuEPO misuse and supports the use of out-of-competition testing of horses in the 2 to 3-day period prior to race-day.

Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics

Targeted protein degradation is the selective removal of a protein of interest through hijacking intracellular protein cleanup machinery. This rapidly growing field currently relies heavily on the use of the E3 ligase cereblon (CRBN) to target proteins for degradation, including the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide which work through a molecular glue mechanism of action with CRBN. While CRBN recruitment can result in degradation of a specific protein of interest (e.g., efficacy), degradation of other proteins (called CRBN neosubstrates) also occurs. Degradation of one or more of these CRBN neosubstrates is believed to play an important role in thalidomide-related developmental toxicity observed in rabbits and primates. We identified a set of 25 proteins of interest associated with CRBN-related protein homeostasis and/or embryo/fetal development. We developed a targeted assay for these proteins combining peptide immunoaffinity enrichment and high-resolution mass spectrometry and successfully applied this assay to rabbit embryo samples from pregnant rabbits dosed with three IMiDs. We confirmed previously reported in vivo decreases in neosubstrates like SALL4, as well as provided evidence of neosubstrate changes for proteins only examined in vitro previously. While there were many proteins that were similarly decreased by all three IMiDs, no compound had the exact same neosubstrate degradation profile as another. We compared our data to previous literature reports of IMiD-induced degradation and known developmental biology associations. Based on our observations, we recommend monitoring at least a major subset of these neosubstrates in a developmental test system to improve CRBN-binding compound-specific risk assessment. A strength of our assay is that it is configurable, and the target list can be readily adapted to focus on only a subset of proteins of interest or expanded to incorporate new findings as additional information about CRBN biology is discovered.

Ketone-based metabolism and signalling in heart failure with preserved ejection fraction (HFpEF)

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – EU funding. Main funding source(s): DZHK Deutsche Forschungsgemeinschaft (DFG-SFB_1470_A02) Cardiac metabolic remodelling in heart failure with preserved ejection fraction (HFpEF) underlies the pathogenesis of this syndrome. Yet, our understanding of metabolic alterations occurring in HFpEF hearts is still limited. Ketone bodies (KBs) – β-hydroxybutyrate (β-OHB) in particular – can become a major, alternative source of fuel for failing hearts. However, the biological relevance of KBs goes beyond their role as energy carrier. We used a ‘two-hit’ mouse model of HFpEF induced by high-fat-diet feeding and L-Name, aiming to evaluate metabolic alteration among various energy substrates (e.g., glucose, fatty acids), in particular the role of β-OHB in HFpEF hearts. Here, we showed that HFpEF heart exhibited impaired glucose oxidation and increased fatty acid oxidation. Impaired glucose oxidation was attributed to the reduced pyruvate dehydrogenase (PDH) activity and increased phospho-PDH expression via the activation of PDH kinase 4 (PDK4). The oxidation of β-OHB was reduced as a result of decreased β-OHB dehydrogenase (BDH1) and succinyl-coA-3-oxaloacid CoA transferase (SCOT) expression. Furthermore, we showed that β-OHB governs mitochondrial function and myocardial bioenergetics in HFpEF, acting as protein modifiers through β-hydroxybutyrylation (Kbhb) – a lysine-based post-translational modification (PTM). Immunoblot analysis for pan- β-hydroxybutyryllysine revealed a significant increase in Kbhb levels in the heart of ‘two-hit’ HFpEF mice compared to control mice. To identify the specific proteins and sites of Kbhb in the heart, Kbhb peptides from control and HFpEF mouse hearts were isolated by immunoaffinity enrichment using a pan-Kbhb antibody-conjugated beads. Volcano plot and gene ontology analysis showed that the most Kbhb-modified proteins in HFpEF hearts are mitochondrial enzymes. Glutamate oxaloacetate transaminase (GOT2) is one of the top hits, participating in the TCA cycle and malate-aspartate shuttle (MAS) in the mitochondria. We further demonstrated that GOT2 activity and MAS were enhacned in the mitochondrial of HFpEF hearts. To conclude, in the heart of ‘two-hit’ model of HFpEF, the oxidation of pyruvate was impaired resulting from decreased PDH activity. The oxidation of β-OHB was also reduced due to the down-regulated BDH1 activity. Instead of oxidation, Kbhb was highlighted as the primary mode of KB utilisation in HFpEF, affecting the GOT2 enzyme activity in MAS pathways. Our results shed light on identifying a novel role of KBs, which can facilitate the understanding of pathogenesis in HFpEF.Ketone-based metabolism and signalling

Targeted Mass Spectrometry for Quantification of Receptor Tyrosine Kinase Signaling.

Targeted proteomics enables sensitive and specific quantification of proteins and post-translational modifications. By coupling peptide immunoaffinity enrichment with targeted mass spectrometry, we have developed the methodology for multiplexed quantification of proteins and phosphosites involved in the RAS/MAPK signaling network. The method uses anti-peptide antibodies to enrich analytes and heavy stable isotope-labeled internal standards, spiked in at known concentrations. The enriched peptides are directly measured by multiple-reaction monitoring (MRM), a well-characterized quantitative mass spectrometry-based method. The analyte (light) peptide response is measured relative to the heavy standard. The method described provides quantitative measurements of phospho-signaling and is generally applicable to other phosphopeptides and sample types.

Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility.

Identification of K-Ras and B-Raf mutations in colorectal cancer (CRC) is essential to predict patients' response to anti-EGFR therapy and formulate appropriate therapeutic strategies to improve prognosis and survival. Here, we combined parallel reaction monitoring (PRM) with high-field asymmetric waveform ion mobility (FAIMS) to enhance mass spectrometry sensitivity and improve the identification of low-abundance K-Ras and B-Raf mutations in biological samples without immunoaffinity enrichment. In targeted LC-MS/MS analyses, FAIMS reduced the occurrence of interfering ions and enhanced precursor ion purity, resulting in a 3-fold improvement in the detection limit for K-Ras and B-Raf mutated peptides. In addition, the ion mobility separation of isomeric peptides using FAIMS facilitated the unambiguous identification of K-Ras G12D and G13D peptides. The application of targeted LC-MS/MS analyses using FAIMS is demonstrated for the detection and quantitation of B-Raf V600E, K-Ras G12D, G13D, and G12V in CRC cell lines and primary specimens.

Significant enhancement of edible Monascus azaphilone pigments production via targeted improvement of the expression of histone deacetylase MrHos2

Monascus azaphilone pigments (MonAzPs) are beneficial secondary metabolites secreted by Monascus spp., which have great potentials to be used in industrial fields besides food industry. But there is very little knowledge about their regulatory mechanism, which limits the large-scale production and utilization of MonAzPs. In this study, we firstly studied the effect on MonAzPs production by inhibiting and enhancing histone deacetylase gene hos2 (Mrhos2) expression in Monascus ruber. UPLC detection revealed that inactivation of Mrhos2 dramatically decreased MonAzPs production, while overexpression of Mrhos2 significantly increased MonAzPs production. Transcriptional level analysis shows Mrhos2 regulates expression of MonAzPs biosynthesis genes. Immunoaffinity enrichment assisted mass spectrometry assay reveals deletion of Mrhos2 perturbs lysine acetylation of enzymes in the metabolic pathway of acetyl-CoA and malonyl-CoA. Collectively, transcription activation and protein acetylation modification mediated by MrHos2 are involved in regulating the MonAzPs production, and MrHos2 can be used as a target to increase MonAzPs production.

Strategy for absolute quantification of phospho‐Tau epitopes in cerebrospinal fluid by mass spectrometry

AbstractBackgroundMass spectrometry is used as reference method for protein quantification by measuring tryptic peptides derived from the target protein relative to a stable isotope‐labeled standard. Existing targeted mass spectrometric methods to measure total tau (tTau) and phosphorylated tau (pTau) species in cerebrospinal fluid (CSF) rely either on immunoaffinity enrichment of the protein or exploit the unusual property of tau being soluble in 2.5% perchloric acid (PA), to precipitate abundant sample proteins. Both strategies, however, carry risk of introducing bias: immunoaffinity enrichment relies on the specificity of the used antibodies, which may not have equal affinity for all of the large number of processed or modified forms of tau, and PA may partially precipitate some tau forms. To address this problem, we have developed an antibody‐ and PA‐free method to measure tau and pTau epitopes in CSF by targeted mass spectrometry.MethodCSF samples (100 µl) from healthy individuals (HC) and Alzheimer’s disease (AD) patients were spiked with stable isotope‐labeled tau peptide standards containing the phospho‐epitopes pTau181, pTau231, pTau217, pTau205, and non‐phosphorylated Tau212‐221, and subjected to tryptic digestion. Desalted samples were fractionated by strong anion‐ and strong cation‐ exchange (SAX and SCX, respectively) solid phase extraction with step‐wise pH elution. The fractions were analyzed by parallel reaction monitoring on a nano‐flow LC‐MS on a Quadrupole‐Orbitrap hybrid mass spectrometer.ResultSeveral tau peptides were detected with both SAX and SCX, including pTau181, pTau217, pTau205, and Tau212‐221. The reproducibility of the new assay was assessed, and its performance was compared with PA‐based sample preparation and immunoassays for tau and pTau in a pilot study of AD patients and controls.ConclusionThe method described here allows for the detection of multiple tau/pTau peptides, while avoiding the need for selective protein isolation methods such as immunoaffinity enrichment or PA precipitation, thereby eliminating bias toward more/less soluble tau species.

Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies

Arginylation is a post-translational modification mediated by the arginyltransferase 1 (ATE1), which transfers the amino acid arginine to a protein or peptide substrate from a tRNA molecule. Initially, arginylation was thought to occur only on N-terminally exposed acidic residues, and its function was thought to be limited to targeting proteins for degradation. However, more recent data have shown that ATE1 can arginylate side chains of internal acidic residues in a protein without necessarily affecting metabolic stability. This greatly expands the potential targets and functions of arginylation, but tools for studying this process have remained limited. Here, we report the first global screen specifically for side-chain arginylation. We generate and validate “pan-arginylation” antibodies, which are designed to detect side-chain arginylation in any amino acid sequence context. We use these antibodies for immunoaffinity enrichment of side-chain arginylated proteins from wildtype and Ate1 knockout cell lysates. In this way, we identify a limited set of proteins that likely undergo ATE1-dependent side-chain arginylation and that are enriched in specific cellular roles, including translation, splicing, and the cytoskeleton.

Quantification of Proteins in Blood by Absorptive Microtiter Plate-Based Affinity Purification Coupled to Liquid Chromatography-Mass Spectrometry.

Liquid chromatography (LC) coupled to mass spectrometry (MS) is increasingly used for quantification of proteins in blood. This development is prompted by ongoing improvements in detection sensitivities of LC-MS instruments and corresponding sample preparation workflows. The combination of immunoaffinity enrichment and targeted LC-MS detection is a notable analytical platform in this regard as it allows for the quantification of low abundance proteins in biological matrices like plasma and serum. Here, we describe such hybrid methods which are based on the enrichment of proteins with antibodies or affimers coupled to adsorptive microtiter plates, the proteolytic digestion of enriched proteins to release protein-specific peptides, and the detection of these peptides by microflow LC coupled to selected reaction monitoring MS.

LC-MS-based detection of silkworm pupae in feed with and without prior immunoaffinity enrichment

Due to their advantageous nutrient composition and high feed conversion efficiency, insects may be an alternative protein source for human and animal nutrition. Recently authorised for feeding purposes in the European Union, silkworm pupae are vastly and cheaply available by-products from sericulture that have been successfully replacing fish meal in aquaculture feed. In order to enable silkworm detection by official control, we firstly identified potential, easily detectable peptide targets from dried silkworm pupae subjected to a standard mass spectrometry (MS)-based bottom-up proteomic workflow. Secondly, a targeted method with an optional immunoaffinity enrichment (IAE) step was developed. Method validation provided a highly reproducible limit of detection of 0.05% (w/w) silkworm pupae in various feeds (aquaculture, poultry, pig) that proved independent from the experimenter and whether IAE was included in sample preparation or not. Furthermore, the method’s specificity and robustness were assessed.

High-throughput immunoaffinity enrichment and N-glycan analysis of human plasma haptoglobin.

Haptoglobin (Hp) is a positive acute phase protein, synthesized in the liver, with four N-glycosylation sites carrying mainly complex type N-glycans. Its glycosylation is altered in different types of diseases but still has not been extensively studied mainly due to analytical challenges, especially the lack of a fast, efficient, and robust high-throughput Hp isolation procedure. Here, we describe the development of a high-throughput method for Hp enrichment from human plasma, based on monolithic chromatographic support in immunoaffinity mode and downstream Hp N-glycome analysis by hydrophilic interaction ultrahigh-performance liquid chromatography with fluorescent detection (HILIC-UHPLC-FLR). Chromatographic monolithic supports in a 96-well format enable fast, efficient, and robust Hp enrichment directly from diluted plasma samples. The N-glycome analysis demonstrated that a degree of Hp deglycosylation differs depending on the conditions used for N-glycan release and on the specific glycosylation site, with Asn 241 being the most resistant to deglycosylation under tested conditions. HILIC-UHPLC-FLR analysis enables robust quantification of 28 individual chromatographic peaks, in which N-glycan compositions were determined by UHPLC coupled to electrospray ionization quadrupole time of flight mass spectrometry. The developed analytical approach enables fast evaluation of total Hp N-glycosylation and is applicable in large-scale studies.

Assessment of KRAS G12C Target Engagement by a Covalent Inhibitor in Tumor Biopsies Using an Ultra-Sensitive Immunoaffinity 2D-LC–MS/MS Approach

KRAS is one of the most frequently mutated oncogenes, with KRAS G12C recently becoming an actionable target for small molecule intervention. GDC-6036 is an investigational KRAS G12C inhibitor that acts by irreversibly binding to the switch II pocket of KRAS G12C when in the inactive GDP-bound state, thereby blocking GTP binding and activation. Assessing target engagement is an essential component of clinical drug development, helping to demonstrate mechanistic activity, guide dose selection, understand pharmacodynamics as it relates to clinical response, and explore resistance. Here, we report the development of an ultra-sensitive approach for assessing KRAS G12C engagement. Immunoaffinity enrichment with a commercially available anti-RAS antibody was combined with a targeted 2D-LC-MS/MS technique to quantify both free and GDC-6036-bound KRAS G12C proteins. A KRAS G12C-positive non-small cell lung cancer xenograft model was dosed with GDC-6036 to assess the feasibility of this assay for analyzing small core needle biopsies. As predicted, dose-dependent KRAS G12C engagement was observed. To date, a sensitivity of 0.08 fmol/μg of total protein has been achieved for both free and GDC-6036-bound KRAS G12C with as little as 4 μg of total protein extracted from human tumor samples. This sub-fmol/μg level of sensitivity provides a powerful potential approach to assess covalent inhibitor target engagement at the site of action using core needle tumor biopsies from clinical studies.

An antibody-free platform for multiplexed, sensitive quantification of protein biomarkers in complex biomatrices

Sensitive, multiplexed protein quantification remains challenging despite recent advancements in LC-MS assays for targeted protein biomarker quantification. High-sensitivity protein biomarker measurements usually require immuno-affinity enrichment of target protein; a process which is highly dependent on capture reagent and limited in capability to measure multiple analytes. Herein, we report a novel antibody-free platform, which measures multiple biomarkers from complex matrices employing a strategically optimized solid-phase extraction cleanup and orthogonal multidimensional LC-MS. Eight human protein biomarkers with different specifications were spiked into canine plasma as a model investigation system. The developed strategy achieved the desired sensitivity, robustness, and throughput via the following steps: (1) post digestion mixed-mode cation exchange-reverse phase SPE enrichment cleaned up the sample initially; (2) rapid, high-pH peptide fractionation further eliminated background components efficiently while selectively enriched signature peptides (SP) to provide sufficient sensitivity for multiple targets; and (3) trapping-micro-LC-MS analysis delivered high sensitivity comparable to a nano-LC-MS method but with much better robustness and throughput for the final analysis. Compared with a conventional LC-MS assay with direct protein digestion and limited clean-up, analysis with this antibody-free platform improved the LLOQ by 1–2 orders of magnitude for the eight protein biomarkers, reaching as low as 5 ng/mL in plasma, with feasible robustness and throughput. This platform was applied for the quantification of biomarkers of respiratory conditions in patients with various lung diseases, demonstrating real-world applicability.

Multiplexed quantification of insulin and C-peptide by LC-MS/MS without the use of antibodies

IntroductionThe measurement of insulin and C-peptide provides a valuable tool for the clinical evaluation of hypoglycemia. In research, these biomarkers are used together to better understand hyperinsulinemia, hepatic insulin clearance, and beta cell function. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an attractive approach for the analysis of insulin and C-peptide because the platform is specific, can avoid certain limitations of immunoassays, and can be multiplexed. Previously described LC-MS/MS methods for the simultaneous quantification of insulin and C-peptide measure the intact analytes and most have relied on immunoaffinity enrichment. These approaches can be limited in terms of sensitivity and interference from auto-antibodies, respectively. We have developed a novel method that does not require antibodies and uses proteolytic digestion to yield readily ionizable proteotypic peptides that enables the sensitive, specific, and simultaneous quantitation of insulin and C-peptide. MethodsSerum samples were precipitated with acetonitrile. Analytes were enriched using solid phase extraction and then digested with endoproteinase Glu-C. Surrogate peptides for insulin and C-peptide were analyzed using targeted LC-MS/MS. ResultsInter-day imprecision was below 20 %CV and linearity was observed down to the lower limit of quantitation for both analytes (insulin = 0.09 ng/mL, C-peptide = 0.06 ng/mL). Comparison to a commercially available insulin immunoassay (Beckman Coulter UniCel DxI 600 Access) revealed a 30% bias between methods. ConclusionA novel LC-MS/MS method for the simultaneous analysis of insulin and C-peptide using Glu-C digestion was developed and evaluated. A detailed standard operating procedure is provided to help facilitate implementation in other laboratories.

Deep 2-Hydroxyisobutyrylome in mouse liver expands the roles of lysine 2-hydroxyisobutyrylation pathway

Lysine 2-hydroxyisobutyrylation (Khib), a newly characterized post-translational modification, is conserved in both eukaryotic and prokaryotic cells. At present, only about 6500 Khib sites have been identified in mammalian cells, which is insufficient compared with the well-known acetylation and thus hinders the understanding of its roles in diverse cellular processes. Here, utilizing immunoaffinity enrichment coupled with LC-MS/MS approach, we carried out a deep proteomics analysis of Khib in mouse liver. A total of 20861 Khib sites in 3768 proteins were identified, which expands the known Khib sites by two folds and represents the deepest Khib proteome in mammalian cells currently. Bioinformatics analysis showed that the 2-hydroxyisobutyrylated proteins have different subcellular localizations and participate in a wide range of molecular functions and cellular processes, such as metabolic processes and disease-related pathways. In addition, RNA-Seq analysis revealed that 1470 genes up-regulated and 790 genes down-regulated in response to elevated Khib levels in HeLa cells. The 1470 up-regulated genes were mainly associated with human papillomavirus infection, ECM-receptor interaction, as well as protein digestion and absorption, while the 790 down-regulated genes were mainly enriched in the multiple diseases and Glycolysis/Gluconeogenesis processes. Taken together, our research largely expands the known Khib sites, which helps delineate the biological functions of the Khib pathway and provides mechanistic insights into how Khib exerts its functions in specific cellular pathways.

Top-Down Mass Spectrometry for Trace Level Quantification of Staphylococcal Enterotoxin A Variants.

We addressed here the need for improved sensitivity of top-down mass spectrometry for identification, differentiation, and absolute quantification of sequence variants of SEA, a bacterial toxin produced by Staphylococcus aureus and regularly involved in food poisoning outbreaks (FPO). We combined immunoaffinity enrichment, a protein internal standard, and optimized acquisition conditions, either by full-scan high-resolution mass spectrometry (HRMS) or multiplex parallel reaction monitoring (PRM) mode. Deconvolution of full-scan HRMS signal and PRM detection of variant-specific fragment ions allowed confident identification of each SEA variant. Summing the PRM signal of variant-common fragment ions was most efficient for absolute quantification, illustrated by a sensitivity down to 2.5 ng/mL and an assay variability below 15%. Additionally, we showed that relative PRM fragment ion abundances constituted a supplementary specificity criterion in top-down quantification. The top-down method was successfully evaluated on a panel of enterotoxin-producing strains isolated during FPO, in parallel to the conventional whole genome sequencing, ELISA, and bottom-up mass spectrometry methods. Top-down provided at the same time correct identification of the SEA variants produced and precise determination of the toxin level. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01710.

Multiplexed Quantitative Analysis of Antibody-Drug Conjugates with Labile CBI-Dimer Payloads In Vivo Using Immunoaffinity LC-MS/MS.

Quantitative analysis of antibody-drug conjugates (ADCs) involves cleavage of ADCs into smaller analytes representing different components and subsequent measurements from multiple assays for a more comprehensive pharmacokinetic (PK) assessment. Multiple PK analytes including the drug remaining conjugated to the antibody (or antibody-conjugated drug, acDrug) and total antibody can be accessed simultaneously using a multiplex assay by proteolytic digestion of an ADC, if the sites of conjugation are homogeneous for an ADC and the linker drug is stable to proteases. Herein, a multiplexed immunoaffinity liquid chromatography-mass spectrometry (LC-MS)/MS PK assay is described involving immunoaffinity enrichment, enzymatic conversion of prodrug, trypsin digestion, and LC-MS/MS as applied to next-generation ADCs constructed from linker drugs bearing dimeric cyclopropabenzindole (CBI) payloads (duocarmycin analogues). The cytotoxic payload is chemically labile, requiring extensive optimization in sample preparation steps to stabilize the drug without ex vivo modification and to convert the prodrug into a single active form of the drug. The qualification data for this assay format showed that this approach provides robust acDrug and total antibody data and can be extended to ADCs with different monoclonal antibody frameworks and linker chemistries. Applications of this multiplexed assay to support preclinical studies are presented.