Journal: RMD Open

Article Title: Immunoglobulins G from Patients with Systemic Sclerosis Modify the Molecular Signatures of Endothelial Cells

doi: 10.1136/rmdopen-2024-004290

Figure Lengend Snippet: Targeted proteomics by automated quantification proteomics approach further characterised ATA+(a) and ATA+(b) group (validation cohort). ( A ) Heatmap represents selected proteins expression among groups. ( B ) Boxplots represent detailed overexpressed proteins in ATA+(a) group both vs ATA+(b) and HC ( B ). NS: non-significant (p value>0.05); *p value<0.05; **p value<0.01; ***p value<0.001; ***p value<0.0001. ATA+, anti-topoisomerase-I positive patients (N=24); ATA+(a), ATA+group a (N=11); ATA+(b), ATA+group b (N=13); ACA+, anti-centromere positive patients (N=18); ARA+, anti-RNA polymerase-III positive patients (N=5); ATA+, anti-topoisomerase-I positive patients; ATA+ (a) , anti-topoisomerase-I positive patients group a; ATA+ (b) , anti-topoisomerase-I positive patients group b; CDH2, cadherin 2; CDH5, VE-cadherin; CISD1, CDGSH iron sulphur domain 1; EIF2B3, eukaryotic translation initiation factor 2B subunit gamma; EPS15, epidermal growth factor receptor pathway substrate 15; FKBP11, FKBP prolyl isomerase 11; HC, healthy controls (N=20); ICAM-1, intercellular adhesion molecule 1; ITGA3, integrin alpha-3; NRBP1, nuclear receptor-binding protein; P4HA2, prolyl 4-hydroxylase subunit alpha-2; PNN, desmosome associated protein; RAE1, Rae1 RNA export 1; SEL1L, adaptor subunit of SYVN1 ubiquitin ligase; SNRPA, small nuclear ribonucleoprotein polypeptide A; STAM, signal transducing adaptor molecule; STK24, serine/threonine-protein kinase 24; TPP1, tripeptidyl-peptidase 1; TTN, titin.

Article Snippet: Boxplots and heatmap for AQUA peptides analysis were performed with GraphPad Prism (V.10.1.0, San Diego, California, USA).

Techniques: Targeted Proteomics, Biomarker Discovery, Expressing, Binding Assay, Ubiquitin Proteomics

Journal: Journal of proteome research

Article Title: HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification

doi: 10.1021/acs.jproteome.7b00005

Figure Lengend Snippet: Performance of HILAQ. (a) The number of NSP identified by HILAQ protocol was significantly increased over QuaNCAT. In the bottom table, confident NSP means the NSP overlapped in all three biological replicates. NSP sensitivity is the ratio of modified peptide/protein identifications over baseline. (**p<0.001; one tailed unpaired t-test, comparison with QuaNCAT) (b) Composition of identified protein by HILAQ and QuaNCAT. (c) Venn diagram analysis on quantification by HILAQ or QuaNCAT. Only proteins quantified confidently by all three replicates of HILAQ or QuaNCAT were counted and compared for this analysis. (d) Normal distribution of replicates of HILAQ and QuaNCAT. All datasets were not normalized. (e) Boxplot analysis on every replicate of HILAQ and QuaNCAT using Graphpad Prism (version 5.01). The boxplot was created with Turkey whiskers. (f) Proteins quantified by all three replicate of HILAQ or QuaNCAT were annotated using web based tool PANTHER (http://pantherdb.org/). There are twiceas many pathways enriched in HILAQ than QuaNCAT. (g) The quantification of NSP between HT22 and HEK293Tcell lines. The peptides ratios from two independent HILAQ experiments were compared. The AHA and HAHA labels were swapped in the two experiments.

Article Snippet: All datasets were not normalized. ( e ) Boxplot analysis on every replicate of HILAQ and QuaNCAT using Graphpad Prism (version 5.01).

Techniques: Modification, One-tailed Test, Comparison