Stable isotopic labeling in proteomics

Gevaert, Kris; Impens, Francis; Ghesquière, Bart; Damme, Petra Van; Lambrechts, Anja; Vandekerckhove, Joël

doi:10.1002/pmic.200800421

Cited by 133 publications

(97 citation statements)

References 71 publications

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“…SILAC and Differential COFRADIC and Mass Spectrometry-COFRADIC proteomics was done as described previously (30,31). ␤-actin WT and ␤-actin KO cells were grown in culture medium supplemented with 12 C, 14 N-or 13 C, 15 N-methionine (Cambridge Isotope Laboratories, Andover, MA) for at least six doubling times (32).…”

Section: Methodsmentioning

confidence: 99%

Cells Lacking β-Actin are Genetically Reprogrammed and Maintain Conditional Migratory Capacity*

Tondeleir

Lambrechts

Müller

et al. 2012

Molecular & Cellular Proteomics

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121

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Vertebrate nonmuscle cells express two actin isoforms: cytoplasmic ␤-and ␥-actin. Because of the presence and localized translation of ␤-actin at the leading edge, this isoform is generally accepted to specifically generate protrusive forces for cell migration. Recent evidence also implicates ␤-actin in gene regulation. Cell migration without ␤-actin has remained unstudied until recently and it is unclear whether other actin isoforms can compensate for this cytoplasmic function and/or for its nuclear role. Primary mouse embryonic fibroblasts lacking ␤-actin display compensatory expression of other actin isoforms. Consistent with this preservation of polymerization capacity, ␤-actin knockout cells have unchanged lamellipodial protrusion rates despite a severe migration defect. To solve this paradox we applied quantitative proteomics revealing a broad genetic reprogramming of ␤-actin knockout cells. This also explains why reintroducing ␤-actin in knockout cells does not restore the affected cell migration. Pathway analysis suggested increased Rho-ROCK signaling, consistent with observed phenotypic changes. We therefore developed and tested a model explaining the phenotypes in ␤-actin knockout cells based on increased Rho-ROCK signaling and increased TGF␤ production resulting in increased adhesion and contractility in the knockout cells. Inhibiting ROCK or myosin restores migration of ␤-actin knockout cells indicating that other actins compensate for ␤-actin in this process. Consequently, isoactins act redundantly in providing propulsive forces for cell migration, but ␤-actin has a unique nuclear function, regulating expression on transcriptional and post-translational levels, thereby preventing myogenic differentiation.

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Section: Methodsmentioning

confidence: 99%

Cells Lacking β-Actin are Genetically Reprogrammed and Maintain Conditional Migratory Capacity*

Tondeleir

Lambrechts

Müller

et al. 2012

Molecular & Cellular Proteomics

Self Cite

121

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“…9 A complete version of the process coded in the MapReduce framework will allow timings to be taken and compared across platforms and Hadoop configurations. This will also allow direct comparison with the desktop computer processing that is currently carried out.…”

Section: Discussion/future Workmentioning

confidence: 99%

Near Real-Time Processing of Proteomics Data Using Hadoop

et al. 2014

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This article presents a near real-time processing solution using MapReduce and Hadoop. The solution is aimed at some of the data management and processing challenges facing the life sciences community. Research into genes and their product proteins generates huge volumes of data that must be extensively preprocessed before any biological insight can be gained. In order to carry out this processing in a timely manner, we have investigated the use of techniques from the big data field. These are applied specifically to process data resulting from mass spectrometers in the course of proteomic experiments. Here we present methods of handling the raw data in Hadoop, and then we investigate a process for preprocessing the data using Java code and the MapReduce framework to identify 2D and 3D peaks.

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“…To find proteins or peptides with significant differences of concentrations in sampled proteomes, different stable heavy isotope labelling techniques can be applied like ICAT, SILAC, iTRAQ or ICPL. Depending on the sample origin, isotope labelling may be performed on different levels (organism, cell, protein, or peptide) and on different reactive groups (Gevaert et al, 2008). As an example, 2DE and ICAT approaches were combined to study the aromatic catabolic pathways in Pseudomonas putida KT 2440.…”

Section: Proteomics As a Tool To Understand The Physiology Of Environmentioning

confidence: 99%

Proteomics as a Tool for the Characterization of Microbial Isolates and Complex Communities

Arsène-Ploetze¹,

Carapito²,

Plewniak³

et al. 2012

Proteomic Applications in Biology

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Stable isotopic labeling in proteomics

Cited by 133 publications

References 71 publications

Cells Lacking β-Actin are Genetically Reprogrammed and Maintain Conditional Migratory Capacity*

Cells Lacking β-Actin are Genetically Reprogrammed and Maintain Conditional Migratory Capacity*

Near Real-Time Processing of Proteomics Data Using Hadoop

Proteomics as a Tool for the Characterization of Microbial Isolates and Complex Communities

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