DIGE Analysis Software and Protein Identification Approaches

Dowling, Paul

doi:10.1007/978-1-0716-2831-7_3

Cited by 3 publications

(2 citation statements)

References 44 publications

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“…The CyDye3- and CyDye5-labeled samples can then be normalized to CyDye2 for the identification of protein spots with different abundance levels when comparing samples [ 91 , 92 , 93 ]. Software packages including DeCyder, SameSpots and Dymension 3 can be incorporated into the workflow to aid in the identification of significant proteins [ 94 , 95 ]. Saturation labeling using CyDye3 and CyDye5 fluorophores with maleimide chemistry can be employed to label all cysteine residues within the sample of interest [ 96 ], enhancing sensitivity compared to the minimal approach [ 90 ].…”

Section: Mass Spectrometry-based Proteomics: Top-down Versus Middle-u...mentioning

confidence: 99%

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Dowling,

Trollet,

Negroni

et al. 2024

Proteomes

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This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.

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Section: Mass Spectrometry-based Proteomics: Top-down Versus Middle-u...mentioning

confidence: 99%

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Dowling,

Trollet,

Negroni

et al. 2024

Proteomes

Self Cite

View full text Add to dashboard Cite

show abstract

“…Various software packages, including DeCyder, SameSpots and Dymension 3, can be used for the determination of protein spot intensity [123][124][125]. The development of DIGE introduced several advantages for using this research platform in protein analysis and has been modified to also study native protein interactions and post-translational modifications [126][127][128].…”

Section: Two-dimensional Gel Electrophoresismentioning

confidence: 99%

Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles

Dowling

Gargan

Swandulla

et al. 2023

IJMS

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The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.

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Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties

Raslan,

Shehata

et al. 2024

Advances in Experimental Medicine and Biology

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DIGE Analysis Software and Protein Identification Approaches

Cited by 3 publications

References 44 publications

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles

Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties

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