Automatic identification of oligonucleotide metabolites in complex biological samples using ultra high-performance liquid chromatography high-resolution mass spectrometry combined with the molecule profiler software.

Oligonucleotide (ON) is one of the rapidly developing fields in biotherapeutics. Ultra high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) has been widely used for the identification of metabolites due to its high sensitivity, high resolution, and ability to provide structural information. The identification of ON metabolites in matrix has been reported by UHPLC-HRMS, however, manual data processing is time-consuming.

Site-Specific Stability Evaluation of Antibody-Drug Conjugate in Serum Using a Validated Liquid Chromatography-Mass Spectrometry Method.

Antibody-drug conjugate (ADC) consists of engineered antibodies and cytotoxic drugs linked via a chemical linker, and the stability of ADC plays a crucial role in ensuring its safety and efficacy. The stability of ADC is closely related to the conjugation site; however, no method has been developed to assess the stability of different conjugation sites due to the low response of conjugated peptides. In this study, an integrated strategy was developed and validated to assess the stability of different conjugation sites on ADC in serum.

Identification of bile acids in snake bile by hydrogen/deuterium exchange mass spectrometry and quantitative structure-retention relationship analysis.

Natural bile acids, a class of steroids with a valeric acid side chain at the C-17 position, present significant challenges in separation and analysis due to structural similarities, isomerism, and large polarity differences. Therefore, advanced analytical methods are essential for the accurate identification and quantification of bile acids. This study conducted a comprehensive qualitative analysis of bile acids by integrating liquid chromatography-tandem mass spectrometry (LC-MS/MS), hydrogen-deuterium exchange tandem mass spectrometry (HDX-MS/MS), and quantitative structure-retention relationship (QSRR) methods.

Direct extraction of ten estrogens from milk samples with DVB/NVP-modified magnetic solid-phase extraction adsorbent followed by pre-column derivatization-UHPLC-MS/MS.

Estrogens and their analogues can cause harm to human health through the food chain. Ten estrogens in different milk samples were directly extracted by amphiphilic divinylbenzene/N-vinyl-2-pyrrolidone (DVB/NVP)-FeO@SiO-based magnetic solid-phase extraction (MSPE) followed by pre-column derivatization and ultra-high performance liquid chromatography tandem mass-spectrometry (UHPLC-MS/MS) detection. Under the optimal conditions, the limits of detection for ten analytes were in the range of 0.

Molecular targets of cisplatin in HeLa cells explored through competitive activity-based protein profiling strategy.

Cisplatin is widely used as anticancer drugs, and DNA is considered as the main target. Considering its high affinity towards cysteines and the important role of cystine containing proteins, we applied a competitive activity-based protein profiling strategy to identify protein cysteines that bind with cisplatin in HeLa cells. Living cells were treated with cisplatin at cytotoxic concentrations, then the protein was extracted.

Identification of endogenous carbonyl steroids in human serum by chemical derivatization, hydrogen/deuterium exchange mass spectrometry and the quantitative structure-retention relationship.

Steroids are tetracyclic aliphatic compounds, and most of them contain carbonyl groups. The disordered homeostasis of steroids is closely related to the occurrence and progression of various diseases. Due to high structural similarity, low concentrations in vivo, poor ionization efficiency, and interference from endogenous substances, it is very challenging to comprehensively and unambiguously identify endogenous steroids in biological matrix.

Qualitative Distribution of Endogenous Cholesteryl Esters in Plasma of Humans and Three Rodent Species Using Stepwise UPLC-Q-Exactive-MS.

Objective: Cholesteryl esters (CEs) are composed of various fatty acyl chains attached to the hydroxyl groups of cholesterol, and abnormalities in their metabolism are related to many diseases. This study aimed to develop an ultrahigh-performance liquid chromatography-quadrupole exactive mass spectrometry (UPLC-Q-Exactive MS) method to identify the CEs in plasma.

Methods: First, the MS fragmentation patterns were investigated using seven commercial CE standards.

Network pharmacology combined with metabolomics and lipidomics to reveal the hypolipidemic mechanism of in hyperlipidemic mice.

(AR), the dried rhizome of (Sam) Juzep, is effective in treating hyperlipidemia, but the mechanisms involved require further exploration. This study evaluated the hypolipidemic properties of AR using an integrated strategy combining network pharmacology with metabolomics and lipidomics. Firstly, a hyperlipidemia mouse model induced by a high-fat diet was established to evaluate the therapeutic effects of AR.

Improved structural annotation of triterpene metabolites of traditional Chinese medicine in vivo based on quantitative structure-retention relationships combined with characteristic ions: Alismatis Rhizoma as an example.

As a fast, sensitive and selective method, liquid chromatography-tandem high-resolution mass spectrometry (LC-HRMS) has been used for studying the in vivo metabolism of traditional Chinese medicine (TCM). However, the rapid discovery and characterization of metabolites, especially isomers, remain challenging due to their complexity and low concentration in vivo. This study proposed a strategy to improve the structural annotation of prototypes and metabolites through characteristic ions and a quantitative structure-retention relationship (QSRR) model, and Alismatis Rhizoma (AR) triterpenes were used as an example.

Quantitative proteomics of plasma and liver reveals the mechanism of turmeric in preventing hyperlipidemia in mice.

Hyperlipidemia is manifested by abnormal levels of circulating lipids and may lead to various cardiovascular diseases. Studies have demonstrated that turmeric supplemented in food can effectively prevent hyperlipidemia. The aim of this study is to elucidate the underlying mechanism.

Interaction of Natural Compounds in Licorice and Turmeric with HIV-NCp7 Zinc Finger Domain: Potential Relevance to the Mechanism of Antiviral Activity.

Nucleocapsid proteins (NCp) are zinc finger (ZF) proteins, and they play a central role in HIV virus replication, mainly by interacting with nucleic acids. Therefore, they are potential targets for anti-HIV therapy. Natural products have been shown to be able to inhibit HIV, such as turmeric and licorice, which is widely used in traditional Chinese medicine.

Fluorescent labeling of sT-incorporated DNA and msU-modified RNA.

We report herein comprehensive investigations of alkylation/sulfur exchange reactions of sulfur-containing substrates including nucleosides such as sU, msU, sU, sA and sT-incorporated DNA enable by comprehensive screenings of the reagents (). It has been proven that iodoacetamide () displays the most promising feasibility toward sulfur-containing substrates including sT, sU, msU, sU and sA. In sharp contrast, the alkylation process with S-benzyl methanethiosulfonate (BMTS, ) displays the best application potential only for sU.

Qualitative distribution of endogenous sphingolipids in plasma of human and rodent species by UPLC-Q-Exactive-MS.

Sphingolipids (SLs) are endogenously bioactive molecules with diverse structures, and its metabolic disorders are involved in the progression of many diseases. In this study, an ultra-performance liquid chromatography quadrupole exactive mass spectrometry (UPLC-Q-Exactive-MS) method was established to comprehensively profile SLs in plasma. First, the fragment patterns of SL standards of each subclass were investigated.

Comprehensive metabolic profiling of triterpenes in rats based on characteristic ions and a triterpene database.

(AR) is widely used in Chinese medicine, and its major bioactive components, triterpenes, reportedly possess various pharmacological activities. Therefore, it is very important to study the metabolism of triterpenes in vivo. However, the metabolism of AR triterpene extract has not been comprehensively elucidated due to its complex chemical components and metabolic pathways.

The Protein-Binding Behavior of Platinum Anticancer Drugs in Blood Revealed by Mass Spectrometry.

Cisplatin and its analogues are widely used as chemotherapeutic agents in clinical practice. After being intravenously administrated, a substantial amount of platinum will bind with proteins in the blood. This binding is vital for the transport, distribution, and metabolism of drugs; however, toxicity can also occur from the irreversible binding between biologically active proteins and platinum drugs.

Preparation of bovine serum albumin restricted access octadecyl/phenyl-mixed-functionalized magnetic silica nanoparticles for magnetic solid phase extraction of antidepressants in aquatic products followed by UHPLC-MS/MS.

Pharmaceuticals are widespread in aquatic ecosystem, which may pose a potential threat to fish and human. In the study, a robust and reliable magnetic solid-phase extraction (MSPE) based on bovine serum albumin (BSA) restricted access octadecyl/phenyl-mixed-functionalized magnetic silica nanoparticles (BSA-C18/Ph-FeO@SiO NPs) as sorbent was developed for the extraction of venlafaxine, paroxetine, fluoxetine, norfluoxetine, sertraline and diphenhydramine from the muscle extracts of aquatic products followed by ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) detection. The homemade sorbent showed appropriate compatibility in aqueous solution and good performance in reducing matrix interference of snakehead muscle tissue extracts with absolute matrix effect ranging in 95.

Discrimination of turmeric from different origins in China by MRM-based curcuminoid profiling and multivariate analysis.

In this research, a three-step strategy was utilized for discriminating turmeric samples from different provinces and regions in China. Firstly, MRM-based UPLC-MS/MS method for chemical profiling of curcuminoids in turmeric samples was established. Then, response surface methodology was applied for optimizing the extraction process of targeted curcuminoids.

Qualitative distribution of endogenous phosphatidylcholine and sphingomyelin in serum using LC-MS/MS based profiling.

PCs and SMs are the major types of glycerophospholipids and sphingophospholipids, the two main categories of phospholipids (PLs). To study the qualitative distribution of serum phosphatidylcholine (PC) and sphingomyelin (SM) in human and three rodent species, liquid chromatography-Orbitrap mass spectrometry (LC-Orbitrap-MS/MS) was used to identify them comprehensively through the accurate mass measurement of both precursor ions and their corresponding product ions. Based on the fragmentation rules of standards, the product ions at m/z 184.

The leaving group in Au(I)-phosphine compounds dictates cytotoxic pathways in CEM leukemia cells and reactivity towards a CysHis model zinc finger.

Gold(i)-phosphine "auranofin-like" compounds have been extensively explored as anticancer agents in the past decade. Although potent cytotoxic agents, the lack of selectivity towards tumorigenic vs. non-tumorigenic cell lines often hinders further application.

Magnetic solid-phase extraction modified Quick, Easy, Cheap, Effective, Rugged and Safe method combined with pre-column derivatization and ultra-high performance liquid chromatography-tandem mass spectrometry for determination of estrogens and estrogen mimics in pork and chicken samples.

In this study, conventional Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method was modified by magnetic solid-phase extraction (MSPE) for purification/pre-concentration of eleven estrogens and estrogen mimics from the extracts of pork and chicken muscles, prior to dansyl chloride (DNS-Cl) derivatization coupled with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) assay. Dual octadecyl- and 2-aminoethyl-3-aminopropyl- groups functionalized mesoporous silica core-shell magnetic nanoparticles (C/NH-FeO@mSiO MNPs) were synthesized and employed as MSPE sorbent with remarkable aqueous compatibility in comparison with conventional C functionalized sorbent. The proposed MSPE is easier to handle than the traditional SPE purification process in QuEChERS method.

Novel PEP-PAN@PSF rods extraction of EDCs in environmental water, sediment, and fish homogenate followed by pre-column derivatization and UHPLC-MS/MS detection.

In the study, novel polysulfone hollow fiber membrane (PSF) supported polar enhanced phase (PEP) particles-polyacrylonitrile (PAN) polymer thin-film rods (PEP-PAN@PSF rods) were developed for the extraction of five steroidal endocrine disrupting chemicals (EDCs) (estrone (E1), estradiol (E2), estriol (E3), ethinyloestradiol (EE2), 2-methoxyestradiol (2ME2)) and four phenolic EDCs (bisphenol A (BPA), hexestrol (HEX), diethylstilbestrol (DES), dienestrol (DE)) in environmental water, sediment, and fish muscle homogenates, followed by pre-column derivatization and ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The traditional preparation method for thin-film rods was improved by introducing a supporting membrane PSF between the external thin-film coating and the internal bare rod, avoiding the conventional pre-corrosion by strong acid/base. The commercial PEP prepared rods showed competitive capacity for both polar and nonpolar EDCs.

Spectrum-effect relationship for anti-tumor activity of shikonins and shikonofurans in medicinal Zicao by UHPLC-MS/MS and chemometric approaches.

Shikonin, shikonofuran and their derivatives are the main bioactive components of Zicao, a traditional Chinese medicine prepared with the dried roots of Lithospermum erythrorhizon, Arnebia euchroma or Arnebia guttata. To establish an efficient and sensitive method for studying material basis of Zicao, different scan modes of ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) and UHPLC triple quadrupole linear ion trap mass spectrometry (QTRAP-MS/MS) were incorporated to make full use of the sensitivity of multiple reaction monitoring (MRM) and overcome its disadvantages. A total of 73 shikonins and shikonofurans compounds were detected in Zicao utilizing various scanning modes.

Intramolecular platinum migration on a peptide in gas phase during collision-induced dissociation.

We report the migration of platinum ligand unit {Pt(en)} (en = ethylenediamine) on a short peptide during collision-induced dissociation fragmentation combined with the characterization of the same species by 2D [H,N] HSQC (Heteronuclear Single Quantum Coherence) NMR spectroscopy. The NMR spectrum showed that the cysteine is platinated while the MS/MS (Tandem mass spectrometry) showed the platination at glutamic acid. Our results provide the first experimental evidence of platinum migration on peptide during collision-induced dissociation.

Identification of the lipid-lowering component of triterpenes from Alismatis rhizoma based on the MRM-based characteristic chemical profiles and support vector machine model.

It has been demonstrated that triterpenes in Alismatis rhizoma (Zexie in Chinese, ZX) contributed to the lipid-lowering effect on high-fat diet-induced hyperlipidemia. Alisol B 23-acetate, one of the abundant triterpenes in ZX, was used as the marker of quality control for ZX in Chinese Pharmacopoeia, while it could not reflect the lipid-lowering effect because other triterpenes in ZX also had prominent medicinal efficacy. To identify the significantly bioactive triterpenes in ZX, a multiple reaction monitoring (MRM)-based characteristic chemical profile (CCP)-support vector machine (SVM) model was used to explore the relationship between triterpenes and lipid-lowering effect of ZX.