Project description:Adult cardiac progenitor/stem cells (CPC/CSC) are multipotent resident populations involved in cardiac homeostasis and heart repair. Assisted by complementary RNAseq analysis, we defined the proteome fraction associable to specific CPC functions by comparison with human mesenchymal stem cells (MSC), the reference population for cell therapy. Label-free proteomics analysis identified 526 proteins expressed differentially in CPC. Quantitative iTRAQ analysis confirmed differential expression of a substantial proportion of these proteins expressed specifically in CPC relative to MSC. Systems biology analysis defined a clear overrepresentation of several categories related to enhanced angiogenic potential. The CPC plasma membrane compartment is comprised by 1595 proteins including a minimal signature of 167 proteins expressed preferentially in CPC. Of these core CPC functions, we selected a panel of 15 predicted cell surface markers and validated high differential expression of CDH5, CD200 and F11R in CPC.
Project description:We developed a sample preparation method for low-input proteomics using lauryl maltose neopentyl glycol. Using the developed method, we performed proteome analysis of 100ng of HEK293T proteins, coIP samples, and serum extracellular vesicles, and further challenged label-free single-cell proteomics of HEK293F cells.
Project description:This dataset includes raw label-free mass spectrometry proteomics data of different sinonasal tumor entities as well as normal sinonasal tissue. 72 samples were processed on a Q Exactive HF-X instrument coupled to an easy nanoLC 1200 system using one microgram of peptides and an 110 minutes gradient.
Project description:Pulmonary arterial hypertension (PAH), a fatal disease, is characterized by pulmonary vascular remodeling and vascular resistance. However, the molecular mechanisms underlying the pathogenesis of PAH remained to be incompletely understood. RNA-seq, 4D Label-free proteomics and phosphoproteomics were used to detect the levels of mRNA, proteins, and phosphoproteins in lung tissues from PAH patients, respectively. Parallel reaction monitoring (PRM) was carried out to verify the expression of the differentially expressed proteins. In total, 967 differentially expressed genes (|log2FoldChange|>1 and p<0.05), 764 differentially expressed proteins and 411 phosphoproteins were observed after data filtering (|log2FoldChange|>1 and p<0.05) in lung tissues of PAH patients as compared with the control group. Integrated analysis of the three omic measures revealed that the biological processes involving inflammation, ion channel and metabolism were closely associated with PAH. Several signaling pathways, such as ferroptosis, HIF-1, PI3K-AKT, and Rap1 might be related to the development of PAH. This study combined multi-omics characteristic profiling to find out the changed genes or proteins that contributed to a detailed pathogenic of PAH. It would have the benefit of looking for the novel and effective treatment targets and therapeutic drugs for PAH patients.
Project description:Urinary proteomics studies have primarily focused on identifying markers of chronic kidney disease (CKD) progression. Here, we aimed to specify CKD-related injury markers through proteomics analysis in urine of patients with CKD. Label-free quantitative proteomics analysis based on liquid chromatography-tandem mass spectrometry was performed on urine samples obtained from 6, 9, 11, and 10 patients in health control, CKD stage 1, 3 and 5, respectively.