Computational protocol: Prognosis of ovarian cancer is associated with effector memory CD8+ T cell accumulation in ascites, CXCL9 levels and activation-triggered signal transduction in T cells

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Protocol publication

[…] OrbiTrap-based mass spectrometry of 7 matched TAT and TAM samples and data analysis by MaxQuant are described in detail elsewhere sample IDs 105, 108, 114, 117, 119, 120, 128, 133). Label-free quantification (LFQ) intensities were used as a measure of protein expression for the analyses in . Mass spectrometry data are deposited at PRIDE (accession No.: PXD006138). [...] Comparative data were statistically analyzed by Student's t-test (two-sided, equal variance; , , S1). Box pots depicting medians (line), upper and lower quartiles (box) range (whiskers) and outliers were constructed using ggplot2 (, S1) or the Seaborn boxplot function (). Correlations were analyzed using the scipy.stat functions. Associations with relapse-free survival (logrank test), hazard ratio (HR) and median survival times were analyzed using the Python Lifelines KaplanMeierFitter and CoxPHFitter functions (, , ). Due to the relatively small sample size we chose a significance threshold of p < 0.01 for all survival analyses Patients suffering from a relapse during first-line chemotherapy (RFS ≤ 3 months) were excluded (n = 1). Functional annotation () was performed by PANTHER gene ontology (GO) enrichment analysis (http://www.http://geneontology.org). […]

Pipeline specifications

Software tools MaxQuant, Ggplot2, Seaborn, PANTHER
Applications Miscellaneous, MS-based untargeted proteomics, Protein sequence analysis
Organisms Homo sapiens
Diseases Neoplasms, Ovarian Neoplasms