Protein identification using nano-HPLC-MS: ESI-MS and MALDI-MS interfaces

Empowering peptidomics: utilizing computational tools and approaches

Bioinformatics plays a critical role in the advancement of peptidomics by providing powerful tools for data analysis, interpretation and integration. Peptidomics is concerned with the study of peptides, short chains of amino acids with diverse biological functions. This area includes peptide identification and characterization, database construction, de novo sequencing, functional annotation, omics data integration and systems biology. Artificial intelligence techniques, such as machine learning and natural language processing, aid in the interpretation of peptide sequence data and the generation of biological insights. By using bioinformatics approaches, peptidomics researchers can accelerate peptide discovery, understand their functions and gain insights into complex molecular interactions.

A Novel Combined Microstrip Resonator/Nanospray Ionization Source for Microwave-Assisted Trypsin Digestion of Proteins

Enzymatic digestion of proteins is a critical step in bottom-up and middle-down proteomics. Here, we demonstrate a method for decreasing the time required for proteolytic digestion of proteins from multiple hours to minutes by using an in-line microstrip cavity for programmed microwave heating. When a nanospray emitter tip, containing a digestion sample, is exposed to a region of highly focused microwave field, the rate of proteolytic digestion is enhanced and the time required for digestion greatly decreased. The design is advantageous for mass spectrometry because the solution-based digestion can then be directly sprayed from a nanoelectrospray tip emitter, decreasing sample transfer loss and allowing the system to be used in a flow-through proteolytic workflow. Microwave-assisted digestion using this method is evaluated against standard overnight digestion protocols using a variety of proteins, evaluating sequence coverage and observed peptide location, digestion rate, and overall efficacy. The influence of applied microwave power is investigated, and enzymatic kinetic parameters are evaluated to estimate temperature within the microreactor. Finally, the modulation of the proteolytic digestion of proteins based upon the modulation of applied microwave power is demonstrated on a time scale of seconds in a flow-through system.

A critical review of microextraction by packed sorbent as a sample preparation approach in drug bioanalysis

Sample preparation is widely accepted as the most labor-intensive and error-prone part of the bioanalytical process. The recent advances in this field have been focused on the miniaturization and integration of sample preparation online with analytical instrumentation, in order to reduce laboratory workload and increase analytical performance. From this perspective, microextraction by packed sorbent (MEPS) has emerged in the last few years as a powerful sample preparation approach suitable to be easily automated with liquid and gas chromatographic systems applied in a variety of bioanalytical areas (pharmaceutical, clinical, toxicological, environmental and food research). This paper aims to provide an overview and a critical discussion of recent bioanalytical methods reported in literature based on MEPS, with special emphasis on those developed for the quantification of therapeutic drugs and/or metabolites in biological samples. The advantages and some limitations of MEPS, as well as its comparison with other extraction techniques, are also addressed herein.

Rapid detection of carbapenem resistance in Acinetobacter baumannii using matrix-assisted laser desorption ionization-time of flight mass spectrometry

Rapid detection of carbapenem-resistant Acinetobacter baumannii strains is critical and will benefit patient care by optimizing antibiotic therapies and preventing outbreaks. Herein we describe the development and successful application of a mass spectrometry profile generated by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) that utilized the imipenem antibiotic for the detection of carbapenem resistance in a large series of A. baumannii clinical isolates from France and Algeria. A total of 106 A. baumannii strains including 63 well-characterized carbapenemase-producing and 43 non-carbapenemase-producing strains, as well as 43 control strains (7 carbapenem-resistant and 36 carbapenem-sensitive strains) were studied. After an incubation of bacteria with imipenem for up to 4 h, the mixture was centrifuged and the supernatant analyzed by MALDI-TOF MS. The presence and absence of peaks representing imipenem and its natural metabolite was analyzed. The result was interpreted as positive for carbapenemase production if the specific peak for imipenem at 300.0 m/z disappeared during the incubation time and if the peak of the natural metabolite at 254.0 m/z increased as measured by the area under the curves leading to a ratio between the peak for imipenem and its metabolite being <0.5. This assay, which was applied to the large series of A. baumannii clinical isolates, showed a sensitivity of 100.0% and a specificity of 100.0%. Our study is the first to demonstrate that this quick and simple assay can be used as a routine tool as a point-of-care method for the identification of A. baumannii carbapenemase-producers in an effort to prevent outbreaks and the spread of uncontrollable superbugs.