Peptidomics and proteogenomics: background, challenges and future needs

Vitorino, Rui; Choudhury, Manisha; Guedes, Sofia; Ferreira, Rita; Thongboonkerd, Visith; Sharma, Lakshya; Amado, Francisco; Srivastava, Sanjeeva

doi:10.1080/14789450.2021.1980388

Cited by 10 publications

(5 citation statements)

References 149 publications

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“…Currently, increasing attention is being made to applying peptidomics to clinical diagnosis and predictive medicine. Peptidomics, an essential branch of proteomics, can be defined as the comprehensive qualitative and quantitative analysis of all endogenous peptides present in cells, tissues or body fluids [122]. The approach was first described by Desiderio et al.…”

Section: Characterization Of Proteins Peptides and Extracellular Part...mentioning

confidence: 99%

“…Peptidomics, an essential branch of proteomics, can be defined as the comprehensive qualitative and quantitative analysis of all endogenous peptides present in cells, tissues or body fluids [122]. The approach was first described by Desiderio et al in 1981 for the MS analysis of picomole amounts of endogenous neuropeptides in canine brain regions and dental pulp tissue and the term peptidomics first appeared in the literature in 2001 [123]. Peptidomics has been described as bridging the link between proteomics and metabolomics [124].…”

Section: Plasma and Urinary Peptidesmentioning

confidence: 99%

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Clinical applications of plasma proteomics and peptidomics: Towards precision medicine

Huang

et al. 2022

Proteomics Clinical Apps

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In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID‐19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID‐19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.

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Section: Characterization Of Proteins Peptides and Extracellular Part...mentioning

confidence: 99%

Section: Plasma and Urinary Peptidesmentioning

confidence: 99%

Clinical applications of plasma proteomics and peptidomics: Towards precision medicine

Huang

et al. 2022

Proteomics Clinical Apps

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“…It includes the investigation of the composition of these proteins, their modifications, interactions, and functional characteristics in the whole organism or in its particular components (organs, cells, tissues, and body fluids) at a certain period of time [1][2][3][4][5]. Peptidomics embraces qualitative and quantitative analysis of all endogenous peptides in biological samples [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

Štěpánová

Kašička

2023

J of Separation Science

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This review gives a wide overview of recent advances and applications of capillary electrophoresis and microchip capillary electrophoresis methods in the fields of proteomics and peptidomics in the period from mid‐2018 up to the end of 2022. The methodological topics covering sample preparation and concentration techniques, hyphenation of capillary electrophoresis methods with mass spectrometry, and multidimensional separations by on‐line or off‐line coupled different capillary electrophoresis and liquid chromatography techniques are described and new developments in both bottom‐up and top‐down approaches in proteomics are presented. In addition, various applications of capillary electrophoresis methods in proteomic and peptidomic studies are demonstrated. They include monitoring of protein posttranslational modifications and applications in biological and biochemical research, clinical peptidomics and proteomics, and food analysis.

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“…The prepared column was used in the separation of a small and medium-sized molecules. With the advancement in the field of peptidomics (study and quantification of endogenous peptides), the separation of peptides has become an essential aspect [8,[27][28][29][30][31][32][33][34][35], but it faces the challenge of adsorption on the capillary surface due to the interaction with silanol groups. To overcome this problem, the Azo-Co-PSS column is being used as a stationary phase and a repeatability study for three standard peptides for different parameters were performed.…”

Section: Introductionmentioning

confidence: 99%

Preparation of open tubular capillary column covalently coated with polystyrene sulfonate with 4,4′‐Azobis(4‐cyanopentanoyl chloride) as polymerization initiator for electrochromatographic separation of alkaloids, sulfonamides, and peptides

Naithani

Cheddah

Yang

et al. 2023

J of Separation Science

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An open tubular capillary electrochromatography column covalently bonded with polystyrene sulfonate was prepared via in situ polymerization using functionalized Azo-initiator 4,4′-Azobis(4-cyanopentanoyl chloride). Scanning electron, fluorescence, and atomic force microscopy techniques showed the formation of a relatively rough layer of polymer. In addition, -CN and C = O stretching vibrations from infrared spectroscopy proved the successful immobilization of the azo-initiator through covalent bonding and X-ray photoelectron spectroscopy confirmed the elemental composition of the formed polymer layer. The prepared column was found to be appropriate for small and medium-sized molecules separation. Compared to bare fused silica capillary column higher selectivity and resolution were obtained for the separation of alkaloids, sulfonamides, and peptides as a result of the electrostatic and pi-pi stacking interactions between the small organic molecules and the coated column without compromising the electroosmotic flow mobility. Separation efficiency was also increased compared to the bare capillary for the separation of alkaloids (about 1.5 times). Moreover, intraday, inter-day, intra-batch, and inter-batch relative standard deviation values of retention time and peak area of peptides were within 2% and 10%, respectively, indicating good repeatability of the column preparation procedure. The developed method for the covalent bonding of polymers through a functionalized azo-initiator could represent a promising stable method for the preparation of an open tubular column.

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Peptidomics and proteogenomics: background, challenges and future needs

Cited by 10 publications

References 149 publications

Clinical applications of plasma proteomics and peptidomics: Towards precision medicine

Clinical applications of plasma proteomics and peptidomics: Towards precision medicine

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

Preparation of open tubular capillary column covalently coated with polystyrene sulfonate with 4,4′‐Azobis(4‐cyanopentanoyl chloride) as polymerization initiator for electrochromatographic separation of alkaloids, sulfonamides, and peptides

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