Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

Pandeswari, Pandi Boomathi; Sabareesh, Varatharajan

doi:10.1039/c8ra07200k

Cited by 56 publications

(41 citation statements)

References 290 publications

(547 reference statements)

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“…Hair Identify ethnic groups [18,36,37] Distinguish gender [26] Distinguish individuals [27,38,39] and middle-down proteomics can be found in some literature reviews (e.g., [58,59] for top-down and [56] for middle-down proteomics). An overview of general methods for bottom-up proteomics is presented in Figure 1 [23].…”

Section: Sample Type Applicationsmentioning

confidence: 99%

Proteomics in Forensic Analysis: Applications for Human Samples

et al. 2021

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Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

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Section: Sample Type Applicationsmentioning

confidence: 99%

Proteomics in Forensic Analysis: Applications for Human Samples

et al. 2021

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“…Currently, mass spectrometry techniques (by means of bottom-up, top-down and middle-down strategies) are able to evaluate the status of protein modification, including their site location (Olsen and Mann 2013;Pascovici et al 2018). The bottom-up MS approach consists of analyzing the resulting peptides (0.8-3 kDa) from previous enzymatic or chemical cleavage and it has been widely used for qualitative analysis of new PTM (Lanucara and Eyers 2013;Pandeswari and Sabareesh 2019). This bottom-up MS approach is a very suitable technique to identify, locate and quantify modified peptides, although it has some limitations mainly concerning the combinatorial effect of several PTM.…”

Section: Techniques To Identify Post-translational Modifications Of Allergensmentioning

confidence: 99%

New applications of advanced instrumental techniques for the characterization of food allergenic proteins

Benedé

Lozano‐Ojalvo

Cristóbal

et al. 2021

Critical Reviews in Food Science and Nutrition

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Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.

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“…In contrast to TD and MD proteomics analysis, for BU data analysis, a deconvolution step is not required when implementing ESI, due to the rare generation of double-and triple-charged fragment ions (36). Mass spectra raw data are commonly processed by Proteome Discoverer or MaxQuant platforms using several search engines, such as Sequest, Mascot, Andromeda, X!Tandem and COMET, usually against UniProt databases (37)(38)(39).…”

Section: Bottom-up Data Analysismentioning

confidence: 99%

Computational Approaches in Proteomics

Cervantes-Gracia

Husi

2019

Computational Biology

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Understanding of biological processes and aberrations in disease conditions has over the years moved away from the study of single molecules to a more holistic and all-encompassing view to investigate the entire spectrum of proteins. This method, termed proteomics, has been enabled principally by mass spectrometry techniques. The power of mass spectrometry-based proteomics lays in its ability to investigate an entire proteome and associated expression or modification states of a huge amount of proteins in one single experiment. This massive amount of data requires a high level of automation in data processing to render it into a reduced set of information that can be used to answer the initial hypotheses, explore the biology or contextualize molecular changes associated with a physiological attribute. This chapter gives an overview of the most common proteomic approaches, biological sample considerations and data acquisition methods, data processing, software solutions for the various steps and further functional analyses of biological data. This enables the comparison of various datasets as a summation of individual experiments, to cross-compare sample types and other metadata. There are many approach pipelines in existence that cover specialist disciplines and data analytics steps, and it is a certainty that many more data analysis methodologies will be generated over the coming years, but it also emphasizes the

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Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

Abstract: Enhanced sequence coverage, better identification of combinatorial co-occurring PTMs and improved detection of proteoforms are key highlights of middle-down approach and hence, this can be a promiscuous approach for protein sequencing and proteomics.

Cited by 56 publications

References 290 publications

Proteomics in Forensic Analysis: Applications for Human Samples

Proteomics in Forensic Analysis: Applications for Human Samples

New applications of advanced instrumental techniques for the characterization of food allergenic proteins

Computational Approaches in Proteomics

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