Summary of the cellular components of the PBMCs phosphoproteins characterized by in-gel IEF LC-MS/MS.

<p>The most enriched cellular components were nuclear proteins and proteins associated with the plasma membrane, cytosol or cytoskeleton. The information was compiled from Gene Ontology annotations.</p

Summary of the molecular functions of the PBMCs phosphoproteins characterized by in-gel IEF LC-MS/MS.

<p>The largest group is constituted by protein binding followed by catalytic activity and nucleic acid binding. The information was compiled from Gene Ontology annotations.</p

Characterization of the Phosphoproteome in SLE Patients

<div><p>Protein phosphorylation is a complex regulatory event that is involved in the signaling networks that affect virtually every cellular process. The protein phosphorylation may be a novel source for discovering biomarkers and drug targets. However, a systematic analysis of the phosphoproteome in patients with SLE has not been performed. To clarify the pathogenesis of systemic lupus erythematosus (SLE), we compared phosphoprotein expression in PBMCs from SLE patients and normal subjects using proteomics analyses. Phosphopeptides were enriched using TiO₂ from PBMCs isolated from 15 SLE patients and 15 healthy subjects and then analyzed by automated LC-MS/MS analysis. Phosphorylation sites were identified and quantitated by MASCOT and MaxQuant. A total of 1035 phosphorylation sites corresponding to 618 NCBI-annotated genes were identified in SLE patients compared with normal subjects. Differentially expressed proteins, peptides and phosphorylation sites were then subjected to bioinformatics analyses. Gene ontology(GO) and pathway analyses showed that nucleic acid metabolism, cellular component organization, transport and multicellular organismal development pathways made up the largest proportions of the differentially expressed genes. Pathway analyses showed that the mitogen-activated protein kinase (MAPK) signaling pathway and actin cytoskeleton regulators made up the largest proportions of the metabolic pathways. Network analysis showed that rous sarcoma oncogene (SRC), v-rel reticuloendotheliosis viral oncogene homolog A (RELA), histone deacetylase (HDA1C) and protein kinase C, delta (PRKCD) play important roles in the stability of the network. These data suggest that aberrant protein phosphorylation may contribute to SLE pathogenesis.</p> </div

KEEG showing differentially-expressed pathways in SLE patients PBMCs versus healty controls.

<p>KEEG showing differentially-expressed pathways in SLE patients PBMCs versus healty controls.</p

The MAPK signaling pathway showing differentially-expressed gene in SLE patients PBMCs versus healthy controls.

<p>Red marks indicate the genes with differential phosphorylation profiles.</p

Connectivity analysis of the SLE-related genes. The connectivity of SRC is the highest one in all related-genes.

<p>Connectivity analysis of the SLE-related genes. The connectivity of SRC is the highest one in all related-genes.</p

Classification of the characterized PBMCs phosphoproteins based on their involvement in biological processes.

<p>The largest group contains proteins related to nucleobase, nucleoside, nucleotide and nucleic acid metabolism. Two other large groups are the proteins involved in cellular component organization and transport. The information was gathered based on Gene Ontology annotations.</p

Demographic and disease manifestation in SLE patients and healthy controls.

<p>Demographic and disease manifestation in SLE patients and healthy controls.</p

Network analysis of SLE-related genes which were indentified in this analysis.

<p>The network can reflect the relationship between genes from the situation as a whole. Blue means expression, gray means binding and purple means ptmod (post-transcription modification).</p

Additional file 5 of Label-free quantitative proteomic analysis of serum exosomes from patients of renal anemia: The Good and the Bad of Roxadustat

Additional file 5: Basic information of differentially expressed proteins verified by PRM