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Table S1. Patient Inclusion Criteria Table details the patient eligibility checklist for the enrolment of patients to the ICORG 06–15 clinical trial. All patients had to meet each criterion listed to be considered for inclusion in the clinical trial.

Figure S1. 1D SDS PAGE of LAP and HAP fractions 1D SDS-PAGE of serum samples depleted serum samples illustrates the effectiveness of abundant protein depletion and normalisation of protein concentration prior to protein digestion and MS analysis. LAP fractions from BF (patient 2) at baseline, remission and failure (lanes 2, 3 and 4 respectively) and patient 8 time matched controls (lanes 5, 6 and 7). Patient 2 baseline HAP fraction is shown in lane 8.

Table S2a. List of proteins from LC-MS/MS Table containing details of all proteins identified and quantified by label free LC-MS analysis. Accession number, protein description, peptide count, peptides used for quantification and confidence score are listed from left to right. In addition the final column indicates which proteins were subsequently measured by MRM.

Table S2b. Additional peptide information for single hit protein identifications The table consists of additional information for any proteins identified by a single peptide. Peptide sequence, confidence score, m/z, charge, mass and mass error of all single peptide identifications are listed.

Table S3. Protein and peptide MRM assay data The table contains a list of the 16 proteins and 2 housekeeping proteins selected for MRM of peptides and the relevant transitions with the precursor ion charge – quadrupole 1, product ion charge – quadrupole 2, collision energy and ion name information. A fragmentor voltage of 130V and dwell time of 20msec was used for all peptide transitions.

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