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Updated: Mar 24, 2026
Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein
Published on: June 30, 2019
SILAC based protein profiling data of MKK3 knockout mouse embryonic fibroblasts
Anup Srivastava1, Amanda S Shinn1, TuKiet T Lam2
1Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520-8057, USA.
Abstract:
This data article reports changes in the phospho and total proteome of MKK3 knock out (MKK3(-) (/) (-)) mouse embryonic fibroblasts (MEFs). The dataset generated highlights the changes at protein level which can be helpful for understanding targets of the MAP kinase signaling pathway. Data was collected after TiO2-based phosphopeptide enrichment of whole cell lysate at baseline condition with bottom-up SILAC-based LC MS/MS quantitative mass spectrometry. We report all the proteins and peptides identified and quantified in MKK3(-/-) and WT MEFs. The altered pathways in MKK3(-/-) MEFs were analyzed by Database for Annotation, Visualization and Integrated Discovery (DAVID, v6.7) and Ingenuity Pathway Analysis (IPA) and are presented as a table and graph, respectively. The data reported here is related to the published work [1]. All the associated mass spectrometry data has been deposited in the Yale Protein Expression Database (YPED) with the web-link to the data: http://yped.med.yale.edu/repository/ViewSeriesMenu.do;jsessionid=6A5CB07543D8B529FAE8C3FCFE29471D?series_id=5044&series_name=MMK3+Deletion+in+MEFs.
Insights
This study details proteomic and phosphoproteomic changes in MKK3 knockout mouse embryonic fibroblasts (MEFs). The findings offer insights into the MAP kinase signaling pathway
Area of Science:
- Proteomics
- Signaling Pathways
- Cell Biology
Background:
- Mitogen-activated protein kinase kinase 3 (MKK3) plays a critical role in stress-induced signaling.
- Understanding MKK3's function requires detailed analysis of its downstream targets at the proteome level.
- MKK3 knockout mouse embryonic fibroblasts (MEFs) provide a model system to investigate MKK3-dependent signaling.
Purpose of the Study:
- To comprehensively analyze the proteome and phosphoproteome of MKK3 knockout MEFs compared to wild-type MEFs.
- To identify proteins and phosphopeptides altered by the absence of MKK3.
- To provide a dataset for understanding MAP kinase signaling pathway targets.
Main Methods:
- Quantitative mass spectrometry (LC-MS/MS) using Stable Isotope Labeling by Amino acids in Cell culture (SILAC).
- TiO2-based phosphopeptide enrichment for phosphoproteome analysis.
- Bioinformatic analysis using DAVID and Ingenuity Pathway Analysis (IPA).
Main Results:
- Identification and quantification of proteins and peptides in MKK3 knockout and wild-type MEFs.
- Dataset highlights changes in total and phospho proteomes.
- Analysis revealed significantly altered pathways in MKK3 knockout MEFs.
Conclusions:
- The generated dataset provides valuable insights into MKK3-dependent proteomic and phosphoproteomic alterations.
- This data can aid in elucidating the targets and mechanisms of the MAP kinase signaling pathway.
- The findings contribute to a deeper understanding of cellular responses to stress and MKK3 function.
