MOESM1 of Quantification of angiotensin II-regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring
Creators: name: Konvalinka, Ana
name: Batruch, Ihor
name: Tokar, Tomas
name: Dimitromanolakis, Apostolos
name: Reid, Shelby
name: Xuewen Song
name: Pei, York
name: Drabovich, Andrei
name: Diamandis, Eleftherios
name: Jurisica, Igor
name: Scholey, James
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 1. Table S1. Characteristics of PCKD patients and healthy controls. *Estimated glomerular filtration rate (eGFR) was calculated from MDRD equation or 24-hour urine creatinine excretion rate. Ď Total kidney volume was calculated by magnetic resonance imaging (MRI). Table S2. Parameters of a multiplex scheduled SRM assay of all monitored peptides, including peptide sequence, m/z, modifications monitored and charge. Table S3. Scheduled SRM parameters of light peptides monitored during method development. Table S4. Modified peptides monitored in urine sample 1. Total areas are calculated as the sum of all heavy-labeled and light peptide areas. Total ratios are calculated by dividing the total heavy by total light area for each peptide. Table S5. Optimized scheduled SRM methods for heavy-labeled and light peptides. Table S6. Associations between urine excretion rate of Ang II-regulated proteins and clinical characteristics such as sex, age and disease group. Numbers represent p-values. For variable sex, two sample t-test was performed. For age, t-test for correlation testing was performed. For disease groups, ANOVA was used. *p&lt;0.05 **p&lt;0.01***p&lt;0.001. Additional file 1: Figure S1. Calibration curves for 7 Ang II-regulated peptides. A) TSP1 peptide TIVTTLQDSIR. y = -0.2239 + 0.2930 x; R2 = 0.9997; B) TSP1 peptide GGVNDFQGVLQNVR. y = 0.06662 + 0.1242 x; R2 = 0.999; C) GLUL peptide. y = 0.08380 + 0.09353 x; R2= 0.9969; D) RHOB peptide. y = 0.3098 + 0.2902 x; R2 = 0.9935; E) BST1 peptide. y = 0.05329 + 0.03982x; R2= 0.9995; F) LYPLA1 peptide. y = 0.2281 + 0.1405 x; R2 = 0.9794; G) LAMB2 peptide. y = -0.2221 + 0.2719 x; R2 = 0.9998. Values at the low range of the curve are shown on the top left. Figure S2. Between-run variability of L/H peptide ratios adjusted for L/H BSA ratios in different A) urine samples (each box represents one urine sample) and B) peptides (each box represents one peptide). X-axis represents log2-transformed adjusted L/H ratios in urine sample A, divided by the L/H ratio in urine sample B. Samples A and B represent aliquots of the same urine sample that were thawed and processed on different days. Log2-transformed ratios thus represent a measure of between-run variability, and perfectly reproducible measurements between samples A and B would have a log2-transformed ratio of 0. Figure S3. Linear correlation between urine excretion rates of two peptides of TSP1. Peptide 1 measurements are presented on x-axis, while peptide 2 measurements are on y-axis. Figure S4. Protein-protein interaction network including the 6 monitored proteins and their direct interaction partners and interaction among them. Physical protein interactions obtained from IID v2016-03 (26516188), and visualization performed in NAViGaTOR 2.3 (19837718). Query proteins are highlighted as rectangles. Nodes with red signify the shortest path connection among query proteins. Node color represent biological function, as per legend. All other nodes and edges are partially transparent to reduce network clutter. Corresponding XML file can be accessed at: http://www.cs.utoronto.ca/~juris/data/ClinProteom16/. Figure S5. Pathway enrichment analysis among the 6 monitored proteins and their PPI partners from Figure S4 using pathDIP ver. 1.0. Only top 60 most significantly enriched pathways taken from sources listed to the right of the graph are displayed. Note, p-values representing significance of some of these pathways were equal to zero, to allow their log10 transformation for visualization purposes, those were adjusted to 10-18.