Integrated proteomics sample preparation and fractionation: Method development and applications

Ye, Xueting; Tang, Jun; Mao, Yiheng; Lu, Xue; Yang, Yun; Chen, Wendong; Zhang, Xinyou; Xu, Rui‐hua; Tian, Ruijun

doi:10.1016/j.trac.2019.115667

Cited by 36 publications

(30 citation statements)

References 91 publications

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“…All steps and buffers required for sample preparation can be integrated for a straightforward and possibly automated sample preparation. Depending on the protein digestion mechanism, three types of integrated sample preparation methods are emerging: (1) in solution digestion, (2) immobilized-enzyme-reactor, and (3) on bed digestion methods [60]. Integrated in-solution digestion methods include filter-aided sample preparation (FASP) that repurposes centrifugal ultrafiltration concentrators in order to remove detergents, perform protein cleavage and isolate peptide fractions [61,62].…”

Section: The Futurementioning

confidence: 99%

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

et al. 2020

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Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.

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Section: The Futurementioning

confidence: 99%

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

et al. 2020

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“…Since then, many high-throughput methods of screening and diagnostic assays have been developed, utilizing them to increase sample throughput, reduce statistical error, and more recently utilize their standard sizing to enable continuous, automated sample preparation and handling [ 41 , 144 , 146 , 147 , 148 ]. Advances in mass spectrometry and its applications to areas such as clinical proteomics, as well as the rise of next-generation sequencing to pathogen metagenomics and antimicrobial stewardship, gave rise to the concept of integrating sample preparation methods with microplates and automation equipment such as pipetting arms [ 41 , 147 , 148 , 149 , 150 , 151 ]. As shown in Figure 11 , many sample preparation methods that have been integrated into microplate platforms are centered around clinical proteomic techniques and, therefore, focus on techniques such as lysis, digestion, separation by molecular weight, or denaturation [ 147 , 152 , 153 , 154 , 155 ].…”

Section: High-throughput Diagnostic Methods In Laboratory Settingsmentioning

confidence: 99%

Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review

Nichols

Geddes

2021

Molecules

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Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.

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“…DNA‐based methods have some limitations related to DNA stability (e.g., the resistance to degradation) and accurate quantitation (Sentandreu & Sentandreu, 2011; Tedeschi et al., 2018), while the DNA extraction procedure is usually complex, time‐consuming, and expensive (von Bargen et al., 2013). Proteinic‐markers‐based methods usually involve intricate multistep operations, including enzymatic digestion, desalting, and peptide fractionation (Ye et al., 2019). To mitigate food fraud, metabolic markers (e.g., metabolites, lipids) were also proposed for food authentication (Dai et al., 2018; Erban et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

Untargeted metabolomics by liquid chromatography‐mass spectrometry for food authentication: A review

Zhong

Wei

et al. 2022

Comp Rev Food Sci Food Safe

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Food fraud is currently a growing global concern with far-reaching consequences. Food authenticity attributes, including biological identity, geographical origin, agricultural production, and processing technology, are susceptible to food fraud. Metabolic markers and their corresponding authentication methods are considered as a promising choice for food authentication. However, few metabolic markers were available to develop robust analytical methods for food authentication in routine control. Untargeted metabolomics by liquid chromatography-mass spectrometry (LC-MS) is increasingly used to discover metabolic markers. This review summarizes the general workflow, recent applications, advantages, advances, limitations, and future needs of untargeted metabolomics by LC-MS for identifying metabolic markers in food authentication. In conclusion, untargeted metabolomics by LC-MS shows great efficiency to discover the metabolic markers for the authenticity assessment of biological identity, geographical origin, agricultural production, processing technology, freshness, cause of animals' death, and so on, through three main steps, namely, data acquisition, biomarker discovery, and biomarker validation. The applica-

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Integrated proteomics sample preparation and fractionation: Method development and applications

Cited by 36 publications

References 91 publications

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review

Untargeted metabolomics by liquid chromatography‐mass spectrometry for food authentication: A review

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