Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics.

Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validating and clinically translating protein biomarkers discovered through global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing the transitions of surrogate endogenous (ENDO) peptides with those of stable isotope-labeled (SIL) peptide counterparts. These methods utilizing amino acid analyzed (AAA) SIL peptides warrant sensitive and precise measurements required for targeted MS assays. Compared with MRM, PRM provides higher experimental throughput by simultaneously acquiring all transitions of the target peptides and thereby compensates for different ion suppressions among transitions of a target peptide. However, PRM still suffers different ion suppressions between ENDO and SIL peptides due to spray instability, as the ENDO and SIL peptides were monitored at different liquid chromatography (LC) retention times. Here we introduce a new targeted MS method, termed wideband PRM (WBPRM), that is designed for high-throughput targeted MS analysis. WBPRM employs a wide isolation window for simultaneous fragmentation of both ENDO and SIL peptides along with multiplexed single ion monitoring (SIM) scans for enhanced MS sensitivity of the target peptides. Compared with PRM, WBPRM was demonstrated to provide increased sensitivity, precision, and reproducibility of quantitative measurements of target peptides with increased throughput, allowing more target peptide measurements in a shortened experiment time. WBPRM is a straightforward adaptation to a manufacturer-provided MS method, making it an easily implementable technique, particularly in complex biological samples where the demand for higher precision, sensitivity, and efficiency is paramount.

Synthesis of S-Carbamidomethyl Cysteine and Its Use for Quantification of Cysteinyl Peptides by Targeted Proteomics.

Proteomics has played a central role in the identification of reliable disease biomarkers, which are the basis of precision medicine, a promising approach for tackling recalcitrant diseases such as cancer, that elude conventional treatments. Among proteomic methodologies, targeted proteomics employing stable isotope-labeled (SIL) internal standards is particularly suited for the clinical translation of biomarker information owing to its high throughput and accuracy in the quantitative analysis of patient-derived proteomes. Using SIL internal standards ensures the utmost level of confidence in detection and precision in targeted MS experiments. For successfully establishing assays based on targeted proteomics, it is crucial to secure broad coverage when selecting the SIL standard peptide panel. However, cysteinyl peptides have often been excluded because of cysteine's high chemical reactivity. To address this limitation, a new cysteine building block was developed by incorporating a sulfhydryl group configured with an S-carbamidomethyl group, which is commonly used in proteome sampling. This compound was found to be chemically stable and applicable to a variety of solid-phase peptide synthesis (SPPS) campaigns. Furthermore, a direct comparison of the synthesized SIL peptides and tryptic endogenous peptides demonstrated the potential utility of an SPPS flow based on the new cysteine building block for improving the success of targeted proteomic applications.

Synthesis, Characterization, and Efficient Catalytic Activities of a Nickel(II) Porphyrin: Remarkable Solvent and Substrate Effects on Participation of Multiple Active Oxidants.

A new nickel(II) porphyrin complex, [NiII (porp)] (1), has been synthesized and characterized by 1 H NMR, 13 C NMR and mass spectrometry analysis. This NiII porphyrin complex 1 quantitatively catalyzed the epoxidation reaction of a wide range of olefins with meta-chloroperoxybenzoic acid (m-CPBA) under mild conditions. Reactivity and Hammett studies, H218 O-exchange experiments, and the use of PPAA (peroxyphenylacetic acid) as a mechanistic probe suggested that participation of multiple active oxidants NiII -OOC(O)R 2, NiIV -Oxo 3, and NiIII -Oxo 4 within olefin epoxidation reactions by the nickel porphyrin complex is markedly affected by solvent polarity, concentration, and type of substrate. In aprotic solvent systems, such as toluene, CH2 Cl2 , and CH3 CN, multiple oxidants, NiII -(O)R 2, NiIV -Oxo 3, and NiIII -Oxo 4, operate simultaneously as the key active intermediates responsible for epoxidation reactions of easy-to-oxidize substrate cyclohexene, whereas NiIV -Oxo 3 and NiIII -Oxo 4 species become the common reactive oxidant for the difficult-to-oxidize substrate 1-octene. In a protic solvent system, a mixture of CH3 CN and H2 O (95:5), the NiII -OOC(O)R 2 undergoes heterolytic or homolytic O-O bond cleavage to afford NiIV -Oxo 3 and NiIII -Oxo 4 species by general acid catalysis prior to direct interaction between 2 and olefin, regardless of the type of substrate. In this case, only NiIV -Oxo 3 and NiIII -Oxo 4 species were the common reactive oxidant responsible for olefin epoxidation reactions.

Synthesis, Characterization, and Catalytic Activities of A Nickel(II) Monoamido-Tetradentate Complex: Evidence For NiIII -Oxo and NiIV -Oxo Species.

A new mononuclear nickel(II) complex, [NiII (dpaq)Cl] (1), containing a tetradentate monoamido ligand, dpaq (dpaq=2-[bis(pyridin-2-ylmethyl)amino]-N-(quinolin-8-yl)acetamide), has been synthesized and characterized by IR spectroscopy, elemental analysis, and UV/Vis spectroscopy. The structure of the nickel complex has been determined by X-ray crystallography. This nonheme NiII complex 1 catalyzed the epoxidation reaction of a wide range of olefins with meta-chloroperoxybenzoic acid (m-CPBA) under mild conditions. Olefin epoxidation using this catalytic system has been proposed to involve a new reactive NiIV -oxo (4) species, based on the evidence from a PPAA (peroxyphenylacetic acid) probe, Hammett studies, H218 O exchange experiments, and ESI mass spectroscopic analysis. Moreover, the nature of solvent significantly influenced partitioning between heterolytic and homolytic O-O bond cleavage of the Ni-acylperoxo intermediate (2). The O-O bond of 2 proceeded predominantly through heterolytic cleavage in a protic solvent, such as CH3 OH. These results suggest that possibly a NiIV -oxo species is a common reactive intermediate in protic solvents. The two active oxidants, namely NiIV -oxo (3) and NiIII -oxo (4), which are responsible for stereospecific olefin epoxidation and radical-type oxidations, respectively, operate in aprotic solvents.

Dinuclear Iron(III) and Nickel(II) Complexes Containing N-(2-Pyridylmethyl)-N'-(2-hydroxyethyl)ethylenediamine: Catalytic Oxidation and Magnetic Properties.

Dinuclear FeIII and NiII complexes, [(phenO)Fe(N3 )]2 (NO3 )2 (1) and [(phenOH)Ni(N3 )2 ]2 (2), were prepared by treating Fe(NO3 )3 ⋅9 H2 O and Ni(NO3 )2 ⋅6 H2 O in methanol, respectively, with phenOH (=N-(2-pyridylmethyl)-N'-(2-hydroxyethyl)ethylenediamine) and NaN3 ; both 1 and 2 were characterized by elemental analysis, IR spectroscopy, X-ray diffraction, and magnetic susceptibility measurements. Two ethoxo-bridged FeIII and two azido-bridged NiII were observed in 1 and 2, respectively; corresponding antiferromagnetic interaction via the bridged ethoxo groups and strong ferromagnetic coupling via the bridged end-on azido ligands within the dimeric unit were observed. Complex 1 did not exhibit any catalytic activity, while 2 exhibited excellent catalytic activities for the epoxidation of aliphatic, aromatic, and terminal olefins.

A new Dual-Channel Chemosensor Based on Chemodosimeter Approach for Detecting Cyanide in Aqueous Solution: a Combination of Experimental and Theoretical Studies.

A new colorimetric and fluorescent receptor 1 for the detection of CN(-) has been simply developed. Receptor 1 showed selectively colorimetric and fluorometric responses to CN(-) in a near-perfect aqueous solution, respectively. This sensor displayed an obvious color change from yellow to colorless upon selective binding with CN(-). In addition, it could function as an "OFF-ON type" fluorescent response through a nucleophilic addition mechanism. The binding mode of receptor 1 with CN(-) was proposed to be 1:1, based on Job plot, (1)H NMR titration and ESI-mass spectrometry analysis. Moreover, the sensing mechanism for CN(-) was theoretically supported by DFT and TD-DFT calculations.