Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery

Cunningham, Robert; Ma, Di

doi:10.1007/s11515-012-1128-z

Cited by 4 publications

(4 citation statements)

References 243 publications

(78 reference statements)

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“…Quantitative proteomics has been combined in several facets to biomarker discovery in a variety of different diseases [98,99]. One example used iTRAQ 8-plex tags to label serum protein digests and identify biomarkers for acute myocardial infarction [100].…”

Section: Biomarker Discoverymentioning

confidence: 99%

Recent advances in isobaric labeling and applications in quantitative proteomics

Sivanich

Tabang

et al. 2022

Proteomics

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Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.

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Section: Biomarker Discoverymentioning

confidence: 99%

Recent advances in isobaric labeling and applications in quantitative proteomics

Sivanich

Tabang

et al. 2022

Proteomics

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“…The most commonly used peptide fragmentation method is collision induced dissociation (CID), highly modified peptides (e.g., glycopeptides) or larger peptides mostly require alternative fragmentation methods such as electron‐transfer dissociation (ETD) and high‐energy collision dissociation (HCD) or a combination of different fragmentation methods (Shen et al, ). A comprehensive overview of all these MS techniques applied in peptidomics can be found in Aristoteli et al (), Cunningham et al (), Dallas et al (), and Romanova et al ().…”

Section: Challenge 3: Mass Spectrometry (Ms) Analysismentioning

confidence: 99%

The challenges of peptidomics in complementing proteomics in a clinical context

Maes

Oeyen

Boonen

et al. 2018

Mass Spectrometry Reviews

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Naturally occurring peptides, including growth factors, hormones, and neurotransmitters, represent an important class of biomolecules and have crucial roles in human physiology. The study of these peptides in clinical samples is therefore as relevant as ever. Compared to more routine proteomics applications in clinical research, peptidomics research questions are more challenging and have special requirements with regard to sample handling, experimental design, and bioinformatics. In this review, we describe the issues that confront peptidomics in a clinical context. After these hurdles are (partially) overcome, peptidomics will be ready for a successful translation into medical practice.

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“…Recently, a N , N ‐dimethylleucine (DiLeu) 4‐plex isobaric tandem mass (MS 2 ) tagging was reported to have high quantitation efficiency, resulting in comparable iTRAQ like data with high protein coverage (up to 43%) and quantitation accuracy (<15%) . This is a promising methodology for multiplex quantitative proteomics because of its low cost compared to the expensive iTRAQ and TMT tags .…”

Section: Quantitative Phosphoproteomicsmentioning

confidence: 99%

Recent advances and challenges in plant phosphoproteomics

2015

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Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.

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Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery

Cited by 4 publications

References 243 publications

Recent advances in isobaric labeling and applications in quantitative proteomics

Recent advances in isobaric labeling and applications in quantitative proteomics

The challenges of peptidomics in complementing proteomics in a clinical context

Recent advances and challenges in plant phosphoproteomics

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