Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC)

Park, Sung Soo; Wu, Wells W.; Zhou, Yu; Shen, Rong-Fong; Martin, Bronwen; Maudsley, Stuart

doi:10.1016/j.jprot.2012.04.035

Cited by 57 publications

(53 citation statements)

References 33 publications

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“…To assess molecular signatures consistent with improved vascular health following Resv supplementation, vascular smooth muscle (VSM) cells from the monkey aorta were isolated, placed in primary culture and then were subjected to quantitative proteomics by stable isotope labeling with amino acids (SILAC) combined with LC-MS/MS, as previously reported (Park et al, 2012). Of the 750 proteins identified, expression of 121 proteins significantly differed in either the HFS and/or HFS+R compared to SD (Table S3C).…”

Section: Resultsmentioning

confidence: 99%

Resveratrol Prevents High Fat/Sucrose Diet-Induced Central Arterial Wall Inflammation and Stiffening in Nonhuman Primates

et al. 2014

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SUMMARY Central arterial wall stiffening driven by a chronic inflammatory milieu accompanies arterial diseases, the leading cause of cardiovascular (CV) morbidity and mortality in Western society. Increase in central arterial wall stiffening, measured as an increase in aortic pulse wave velocity (PWV), is a major risk factor for clinical CV disease events. However, no specific therapies to reduce PWV are presently available. In rhesus monkeys, a two-year diet high in fat and sucrose (HFS) increases not only body weight and cholesterol, but also induces prominent central arterial wall stiffening and increases PWV and inflammation. The observed loss of endothelial cell integrity, lipid and macrophage infiltration, and calcification of the arterial wall were driven by genomic and proteomic signatures of oxidative stress and inflammation. Resveratrol prevented the HFS-induced arterial wall inflammation and the accompanying increase in PWV. Dietary resveratrol may hold promise as a novel therapy to ameliorate increases in PWV.

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Section: Resultsmentioning

confidence: 99%

Resveratrol Prevents High Fat/Sucrose Diet-Induced Central Arterial Wall Inflammation and Stiffening in Nonhuman Primates

et al. 2014

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“…This may be overcome by increasing the concentration of proline in the media as described by Park et al [30]. …”

Section: Methodsmentioning

confidence: 99%

Exploring G protein-coupled receptor signaling networks using SILAC-based phosphoproteomics

Williams

Bethard

Berkaw

et al. 2016

Methods

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The type 1 parathyroid hormone receptor (PTH1R) is a key regulator of calcium homeostasis and bone turnover. Here, we employed SILAC-based quantitative mass spectrometry combined with bioinformatic pathways analysis to examine global changes in protein phosphorylation following short-term stimulation of endogenously expressed PTH1R in osteoblastic cells in vitro. Following 5 min exposure to the conventional agonist, PTH(1-34), we detected significant changes in the phosphorylation of 224 distinct proteins. Kinase substrate motif enrichment demonstrated that consensus motifs for PKA and CAMK2 were the most heavily upregulated within the phosphoproteome, while consensus motifs for mitogen-activated protein kinases were strongly downregulated. Signaling pathways analysis identified ERK1/2 and AKT as important nodal kinases in the downstream network and revealed strong regulation of small GTPases involved in cytoskeletal rearrangement, cell motility, and focal adhesion complex signaling. Our data illustrate the utility of quantitative mass spectrometry in measuring dynamic changes in protein phosphorylation following GPCR activation.

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“…Additional features have also been included for quantification using metabolic labeling (e.g., 15 N, SILAC). Among these are the calculation of a reverse ratio for the label swap experimental setup [56, 57] and the assessment of the statistical significance of differentially expressed peptides. More recently, improvements were implemented in Census 2 for the calculation of 15 N enrichment ratios.…”

Section: Computational Pipelinementioning

confidence: 99%

From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics

Lavallée‐Adam

Park

Martínez‐Bartolomé

et al. 2015

J. Am. Soc. Mass Spectrom.

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In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development.

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Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC)

Cited by 57 publications

References 33 publications

Resveratrol Prevents High Fat/Sucrose Diet-Induced Central Arterial Wall Inflammation and Stiffening in Nonhuman Primates

Resveratrol Prevents High Fat/Sucrose Diet-Induced Central Arterial Wall Inflammation and Stiffening in Nonhuman Primates

Exploring G protein-coupled receptor signaling networks using SILAC-based phosphoproteomics

From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics

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