4DSmartDIA protein quantification omics of two mouse IP elution samples (no duplication)

ABSTRACT: Based on the Raw files obtained by mass spectrometry detection, 1) Construct a sample-specific protein database according to the source of the samples, and then conduct database search using analysis software; 2) Conduct quality control analysis at the peptide and protein levels based on the results of database search; 3) Conduct quantitative analysis of proteins, including quantitative distribution and repeatability analysis; 4) Perform common functional annotations on the identified proteins, including GO, KEGG, Protein domain, COG/KOG, STRING database annotations, etc. 6) Functional classification statistical analysis of proteins between the two groups was conducted, including GO secondary classification, subcellular localization classification, COG/KOG classification and KEGG pathway classification statistics; 7) The Fisher's exact test method was used to conduct enrichment analysis on the differentially expressed proteins between the two groups, involving the functions of GO, KEGG and Protein domain; 8) When the project has multiple experimental groups, the functional relationships of differentially expressed proteins under different experimental conditions are compared through rich cluster analysis. 9) Through Protein-protein interaction network (PPI) analysis, the key regulatory proteins under specific experimental conditions were screened out.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Stem Cell, Cell Culture

SUBMITTER: Xinyue Li  

LAB HEAD: Xinyue Li

PROVIDER: PXD063853 | Pride | 2026-06-15

REPOSITORIES: Pride