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Figure S1. LC-MRM Assay Development. Serum protein electrophoresis (SPEP) indicates the presence of the monoclonal antibody produced by multiple myeloma tumor cells (box); immunofixation reveals the type of antibody associated with the disease, in this case, IgG/Lambda (A). After 18 months of storage as required for patient care, SPEP bands were excised, digested with trypsin, and sequenced with LC-MS/MS on a quadrupole time-of-flight mass spectrometer; representative data are shown for the peptide, ALPAPIEK, from IgG1 shown (B). The most consistently observed peptides from each heavy and light antibody chain were translated to quantitative LC-MRM assays (C). Stable isotope-labeled standards (SIS) were synthesized for the most sensitive and specific peptides.

Figure S2. Quality Control Data for IgA Peptide, WLQGSQELPR. Three point reverse calibration curves were used to bracket every 10 samples (A). One batch is expanded and color coded to show the individual replicates (B). Each sample was analyzed in triplicate, but each batch was run from sample 1 to sample 10 prior to the replicate LC-MRM analyses; data are presented for triplicate analysis of all 83 samples (C).

Figure S3. Comparison of Immunoglobulin Quantification Methods. Nephelometry measurements are compared with SPEP (A). LC-MRM protein quantification is compared with SPEP (B). In both cases, the quantification of the entire level of immunoglobulin expression exceeds the amount measured for the monoclonal protein by SPEP (slopes > 1), and both nephelometry and LC-MRM show limited correlation with SPEP.

Figure S4. Comparison of LC-MRM Quantification of Immunoglobulin Heavy Chains in Two Different Batches.

Figure S5. Assembly of the Immunoglobulin Kappa Protein

Figure S6.

Figure S7.

prca1545-sup-0002-SupMat.xls61KTable S1.
prca1545-sup-0003-SupMat.xlsx17KTable S2. QC Metrics for RNA-sequencing of MM Patient Samples.

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