Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin

Laštovičková, Markéta; Bobáľ, Pavel; Strouhalová, Dana; Bobáľová, Janette

doi:10.1016/j.ab.2019.01.004

Cited by 3 publications

(1 citation statement)

References 26 publications

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“…Appropriate enzymatic digestion conditions (e.g. enzymes, time, temperature, and pH) can effectively result in the stable and high recovery of peptides from target antibody via enzymatic hydrolysis, thus enhancing the sensitivity of antibody drugs and endogenous protein (Lastovickova, Bobal, Strouhalova, & Bobalova, ). An, Zhang, Johnson, and Qu () have described a direct surfactant‐aided‐precipitation/on‐pellet‐digestion (SOD) method that exhibits higher peptide recovery in various complex matrices compared with three commonly applied methods (i.e., filter to assist sample preparation, in‐gel digestion, and in‐solution digestion).…”

Section: Sample Clean‐up and Recoverymentioning

confidence: 99%

Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies

Chen

Gao

Zhong

2020

Biomedical Chromatography

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Chromatographic method has long been recognized as the most widely used separation method in bioanalytical research. However, the relatively low sensitivity of existing chromatographic methods remains a significant challenge, as the requirements for experimental procedures become more demanding. This review discusses the main causes for the low sensitivity of chromatographic methods and aims to introduce different technologies for enhancing their sensitivity in the following aspects: (i) different pretreatment methods for improving clean‐up efficiency and recovery; (ii) derivatization step for altering the chromatographic behavior of analytes and enhancing MS ionization efficiency; (iii) optimal LC–MS conditions and appropriate separation mechanism; and (iv) applications of other chromatographic methods, including miniaturized LC, 2D‐LC, 2D‐GC, and supercritical fluid chromatography. Altogether, this review is devoted to summarizing the recent technologies reported in the literature and providing new strategies for the detection of bioanalytes.

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Section: Sample Clean‐up and Recoverymentioning

confidence: 99%

Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies

Chen

Gao

Zhong

2020

Biomedical Chromatography

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Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network

Ciordia,

Santos,

Dias

et al. 2024

Talanta

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Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva

2022

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This research aimed to find an efficient and repeatable bottom-up proteolytic strategy to process the unstimulated human saliva. The focus is on monitoring immune system activation via the cytokine and interleukin signaling pathways. Carbohydrate metabolism is also being studied as a possible trigger of inflammation and joint damage in the context of the diagnostic procedure of temporomandibular joint disorder. The preparation of clean peptide mixtures for liquid chromatography–mass spectrometry analysis was performed considering different aspects of sample preparation: the filter-aided sample preparation (FASP) with different loadings of salivary proteins, the unfractionated saliva, amylase-depleted, and amylase-enriched salivary fractions. To optimize the efficiency of the FASP method, the protocols with the digestion in the presence of 80% acetonitrile and one-step digestion in the presence of 80% acetonitrile were used, omitting protein reduction and alkylation. The digestion procedures were repeated in the standard in-solution mode. Alternatively, the temperature of 24 and 37°C was examined during the trypsin digestion. DyNet analysis of the hierarchical networks of Gene Ontology terms corresponding to each sample preparation method for the bottom-up assay revealed the wide variability in protein properties. The method can easily be tailored to the specific samples and groups of proteins to be examined.

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Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin

Cited by 3 publications

References 26 publications

Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies

Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies

Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network

Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva

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