SILAC based protein profiling data of MKK3 knockout mouse embryonic fibroblasts

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.