Identification of the differentially abundant peptides was performed by measuring all samples using the nanoLC-ESI-Orbitrap. Due to the prefractionating by nanoLC far more peak masses and identifications are generated by ESI-Orbitrap than there are peak masses in the analysis matrix generated by quantitative MALDI-FT-ICR. Although many of the identified peptides do not correspond to peak masses in the analysis matrix, we were able to identify a number of differentially abundant peptides for all three comparisons (full list, including charge states and sequence coverage, can be found in the supplementary material (Supplementary Information Mass Spectrometry S1 file)). Of the 43 differentially abundant peptide masses that were observed using MALDI-FT-ICR mass spectrometry in the comparison of PP MScl versus the controls we were able to identify 29 peptides (Supplementary Information Table S1 ). These peptides included several peptides of Ig gamma-1 and Ig kappa. Another differentially abundant peptide was identified as a part apolipoprotein D, which has previously been shown to be elevated intrathecally in MScl patients [17] . In the comparison of RR MScl versus controls we were able to identify 24 of the 41 differentially abundant peptide masses, which, as was the case with the 