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Figure S1. Identification of differential peaks highlighted We identified the peaks 1-5 by fraction collection and MS/MS fragmentation analysis. Identified peaks were isolated by the use of fraction collector after reverse phase chromatography (Fig. S1 A). In Fig. S1 B was shown deconvoluted ESI+-Mass-Spectrum of the chromatographic peak eluted between 42 and 43 minutes showing a low intense 13761 Da signal of the free monomer TTR; the major molecular species at 13793 Da (differential peak 2 showed in Fig. 1) and 13841 Da (differential peak 3, showed in Fig. 1). The fraction containing interesting peaks was analysed by μLC-nano-ESI-Q-TOF fragmentation analysis. All peaks were identified as TTR, a very abundant protein in CSF. Fig. S1 C highlights tandem mass spectra and reconstructed sequences of TTR peptides found in the chromatographic fraction analysed after digestion with Tryspin. Details of identification experiments are shown in Table S2.

Figure S2. Serum TTR profiling We analysed the serum taken at the same time of CSF to verify the presence of the differential isoforms in peripheral compartment, for all MS patients included in the casuistry. As shown in Fig S2 A average spectrum of CSF (upper profile) differs from the serum profiling (lower profile). Peaks 1, 4 and 5 are visible in both biological fluids corresponding to canonical TTR isoforms. Peaks 2 and 3 emerge only in CSF profile. This result is clear in Fig S2 B and C where intensity of peak 2 and 3 (13793 Da and 13841 Da, respectively) in each acquired spectrum is shown. The arrow indicates separation from CSF to serum samples.

Table S1. Clinical data from patients affected by multiple sclerosis

Table S2. Tandem Mass Spectrometry experiments

Table S3. molecular weights of PTMs

Table S4. Correlation between TTR isoforms and anomalous TTR dimer

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