Project description

Sample processing protocol

HK2 cells were stimulated and supernatant prepared as described in the publication. Mass spectrometry analysis was performed on a high-resolution LC-MS system (Eksigent nanoLC 425 coupled to a Triple-TOF 6600, AB Sciex) in information dependent acquisition (IDA) mode. For detailed information, see supplemental methods.

Data processing

The analysis of MS runs was performed using MaxQuant version 1.6.0.16 (Cox and Mann, 2008). Library generation for peptide spectrum matching was based on Homo sapiens. Oxidation of methionine and acetylation of the N-terminus were considered as peptide modifications. Minimal peptide length was set to 6 amino acids, the maximal mass to 6000 Da. Thresholds for peptide spectrum matching and protein identification were set by a false discovery rate (FDR) of 0.01.

Statistics

Data represent means +/- SEM. Statistical differences were determined by factorial analysis of variance followed by Tukey's or Dunnett's multiple comparison test. In the case of two means, classical t test analyses were used. Two-way ANOVA followed by Bonferroni's multiple comparison tests were performed. All statistical analyses were performed using GraphPad Prism 9.0.

Data files

Overview of significantly Oxa-regulated proteins in cell culture supernatant of TGF-b induced HK2 cells can be found at "runs\Proteomics\Book1_Secretome_TGF_Oxa_log2Ratio_Er.xlsx".

Additional details

Lab

• Name: Gerhard Erkel
• Email: erkel@rptu.de
• Affiliation: Molecular Biotechnology & Systems Biology, RPTU Kaiserslautern, Kaiserslautern, Germany