Longitudinal Proteomics Analysis of Cerebrospinal Fluid in Survivors of Childhood Acute Lymphoblastic Leukemia

Mass spectrometry-based proteomic profiling of cerebrospinal fluid (CSF) in large patient cohorts, particularly among childhood cancer survivors, remains scarce, limiting opportunities for benchmarking, method development, and validation. Here, we present a longitudinal CSF proteomics dataset from survivors of childhood acute lymphoblastic leukemia (ALL). Samples were collected from 178 patients enrolled in the TOTXVI therapeutic protocol at two timepoints: diagnosis (pre-treatment) and during the consolidation phase of chemotherapy (totaling 356 samples). CSF proteomes were profiled using tandem-mass-tag (TMT) labeling coupled with extensive fractionation and high-resolution liquid chromatography-tandem mass spectrometry (LC/LC-MS/MS). The dataset includes quantitative profiles for more than 3,000 confidently identified unique proteins. This resource enables the investigation of chemotherapy-induced alterations in the CSF proteome and provides a valuable resource for studying the molecular mechanisms of neurotoxicity, identifying biomarkers of adverse late effects, and guiding the development of neuroprotective strategies in childhood cancer survivors.