Generation of a mouse SWATH-MS spectral library to quantify 10148 proteins involved in cell reprogramming

Area of Science:

• Proteomics
• Stem Cell Biology
• Biotechnology

Background:

• Murine models are crucial for biological and pathological studies.
• Quantitative proteomic analysis, particularly Data Independent Acquisition (DIA) methods like SWATH-MS, is increasingly used for large-scale sample analysis.
• Induced pluripotent stem cells (iPSCs) derived from fibroblasts undergo significant proteomic alterations.

Purpose of the Study:

• To create a comprehensive mouse proteome reference library for quantitative proteomic studies.
• To support research involving induced pluripotency in stem cells.
• To provide a reproducible method for library generation.

Main Methods:

• Development of a reference library using SWATH-MS.
• Generation of mass spectra for proteomic profiling.
• Creation of an extensively documented script for library replication and adaptation.

Main Results:

• The library provides deep coverage of the mouse proteome, including 29,519 proteins (53% of the proteome).
• 7,435 proteins (13%) are supported by a proteotypic peptide within the library.
• A documented script enables replication and adaptation of the library generation process.

Conclusions:

• The generated mouse proteome library is a valuable resource for quantitative proteomic studies, especially in stem cell research.
• The reproducible methodology facilitates data reuse and adaptation for novel applications.
• This resource deepens the understanding of proteomic changes in biological systems like induced pluripotency.