Immunodepletion and digestion of CSF replication 3 samples have been previously described by Dayon and colleagues (45 (link), 46 (link)). The remaining replication samples were not individually immunodepleted. These nondepleted samples were digested in trypsin as previously described (17 (link)). For each replication analysis, 120 μl of aliquots of eluted peptides from each sample were pooled together and split into equal volume aliquots for use as the global internal standard (48 (link)) for TMT labeling. All individual samples and the pooled standard were dried by speed vacuum (Labconco). To boost the signal of low abundance CSF proteins, a “boost” sample [i.e., a biological sample mimicking study samples but accessible in a much larger quantity (37 (link), 69 (link))] was prepared for each replication analysis by combining 125 μl from each sample into one pooled CSF sample (17 (link)). This pooled sample was subsequently immunodepleted using 12 ml of High Select Top14 Abundant Protein Depletion Resin (Thermo Fisher Scientific, A36372), digested as described above, and included in subsequent multiplex TMT labeling.