Recent advances in isobaric labeling and applications in quantitative proteomics

Sivanich, Michael K.; Gu, Ting‐Jia; Tabang, Dylan Nicholas; Li, Lingjun

doi:10.1002/pmic.202100256

Cited by 44 publications

(44 citation statements)

References 179 publications

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“…The Peptide Quantification section discusses some label-based quantification methods and cites works that give more details, including reviews/comparisons − and state-of-the-art methods. ,,, One approach not discussed above is the use of chemical (as opposed to metabolic) non-isobaric stable isotope labeling reactions such as lysine dimethylation. This is a low-cost alternative to isobaric labeling especially helpful in pairwise comparisons where SILAC is not feasible .…”

Section: Advanced Topics and Further Readingmentioning

confidence: 99%

An Introduction to Mass Spectrometry-Based Proteomics

Shuken

2023

J. Proteome Res.

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Mass spectrometry is unmatched in its versatility for studying practically any aspect of the proteome. Because the foundations of mass spectrometry-based proteomics are complex and span multiple scientific fields, proteomics can be perceived as having a high barrier to entry. This tutorial is intended to be an accessible illustrated guide to the technical details of a relatively simple quantitative proteomic experiment. An attempt is made to explain the relevant concepts to those with limited knowledge of mass spectrometry and a basic understanding of proteins. An experimental overview is provided, from the beginning of sample preparation to the analysis of protein group quantities, with explanations of how the data are acquired, processed, and analyzed. A selection of advanced topics is briefly surveyed and works for further reading are cited. To conclude, a brief discussion of the future of proteomics is given, considering next-generation protein sequencing technologies that may complement mass spectrometry to create a fruitful future for proteomics.

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Section: Advanced Topics and Further Readingmentioning

confidence: 99%

An Introduction to Mass Spectrometry-Based Proteomics

Shuken

2023

J. Proteome Res.

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“…aegypti , using isobaric-labeled quantitative proteomics. Mass spectrometry-based proteomics are highly effective for assessing host-pathogen interactions (also reviewed in ( Sivanich et al., 2022 ). Isobaric labeling quantitative methods allow for multiplexing, which allows for: higher throughput, increased statistical robustness, sample conservation, high coverage depth, and increased efficiency.…”

Section: Disease Transmission By Insect Vectorsmentioning

confidence: 99%

Editorial: The application of OMICS technologies to interrogate host-virus interactions

Gomes

Alfson²,

Junqueira³

2022

Front. Cell. Infect. Microbiol.

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Editorial on the Research TopicThe application of OMICS technologies to interrogate hostvirus interactionsViruses can infect all types of life forms, ranging from humans to bacteria. Highcontent data generated with omics technologies can be used to identify emergent properties of these systems, providing targets for further mechanistic investigations. Since the completion of the first genome sequencing projects, omics approaches have been used to study the dynamics and complexity of host-virus interactions. Starting with early microarray studies aiming to cover a fraction of the host genome and progressively moving into deep-sequencing projects, these studies shed light on the modulation of host gene expression profiles upon infection. In addition, changes in the protein level could be accessed via mass spectrometry-based proteomic methods (Luo and Muesing 2014), applied on a genome scale [reviewed in (Lum and Cristea, 2016)]. These investigations allowed direct protein quantification that partially validated previous transcriptomic findings and highlighted the complexity of the regulation of protein translation and post-translation modifications during virus infection (Hoogendijk et al., 2019;Kumar et al., 2020). More recently, network analysis has been progressively used to identify promising targets for therapeutic interventions and drug repurposing, and is now playing a role in vaccine development studies (Hagan et al., 2015;Pulendran et al., 2021). At the same time, reduced sequencing costs and evolving hardware capabilities now allow for massive projects involving multi-omics data integration (Sammut et al., 2022) and reviewed in (Wang et al. 2019;Appiasie et al., 2021). Therefore, this Research Topic discloses the state-of-the-art omics technology applied to virus-host interactions. It introduces five selected articles from Frontiers in Cellular and Infection Microbiology frontiersin.org 01

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“…Additionally, specific information about peptide sequences with various post-translational modifications can be obtained. LC-MS/MS can also be used to quantify neuropeptides through multiple approaches, such as label-free quantitation, isobaric labeling quantitation, and isotopic labeling quantitation …”

Section: Introductionmentioning

confidence: 99%

Global Neuropeptidome Profiling in Response to Predator Stress in Rat: Implications for Post-Traumatic Stress Disorder

Wenxin

Ibarra

et al. 2023

J. Am. Soc. Mass Spectrom.

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Traumatic stress triggers or exacerbates multiple psychiatric illnesses, including post-traumatic stress disorder (PTSD). Nevertheless, the neurophysiological mechanisms underlying stress-induced pathology remain unclear, in part due to the limited understanding of neuronal signaling molecules, such as neuropeptides, in this process. Here, we developed mass spectrometry (MS)-based qualitative and quantitative analytical strategies to profile neuropeptides in rats exposed to predator odor (an ethologically relevant analogue of trauma-like stress) versus control subjects (no odor) to determine peptidomic alterations induced by trauma. In total, 628 unique neuropeptides were identified across 5 fear-circuitry-related brain regions. Brain-region-specific changes of several neuropeptide families, including granin, ProSAAS, opioids, cholecystokinin, and tachykinin, were also observed in the stressed group. Neuropeptides from the same protein precursor were found to vary across different brain regions, indicating the site-specific effects of predator stress. This study reveals for the first time the interaction between neuropeptides and traumatic stress, providing insights into the molecular mechanisms of stress-induced psychopathology and suggesting putative novel therapeutic strategies for disorders such as PTSD.

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Recent advances in isobaric labeling and applications in quantitative proteomics

Cited by 44 publications

References 179 publications

An Introduction to Mass Spectrometry-Based Proteomics

An Introduction to Mass Spectrometry-Based Proteomics

Editorial: The application of OMICS technologies to interrogate host-virus interactions

Global Neuropeptidome Profiling in Response to Predator Stress in Rat: Implications for Post-Traumatic Stress Disorder

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