init ARC structure; add data

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README.md

+
+### 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
+
+|Meta data|Description|
+|--|--|
+|Experiment type| Gel based proteomics|
+|Species| Homo sapiens|
+|Tissue| cell culture |
+|Instrument | TripleTOF 6600 (MS:1002533)|
+|Modification | L-methionine sulfone (), acetylated residue (MOD:00394)|
+|Quantification | MS1 intensity based label-free quantification method (PRIDE:0000425)|
+|Cell type |HK2 cell line|
+|Disease| None|
+
+### Lab
+
+- Name: Gerhard Erkel
+- Email: erkel@rptu.de
+- Affiliation: Molecular Biotechnology & Systems Biology, RPTU Kaiserslautern, Kaiserslautern, Germany
+
+
+
+