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Submitted on October 7, 2005
Plasma Proteome Institute, Washington, DC 20009-3450
Corresponding Author: leighanderson{at}plasmaproteome.org
Quantitative LC-MS/MS assays have been designed for tryptic peptides representing 53 high and medium abundance proteins in human plasma using a multiplexed MRM approach. Of these, 47 produced acceptable quantitative data, demonstrating within-run CV’s (n=10) of 2-22% (78% of assays had CV < 10%). A number of peptides gave CV’s in the range 2-7% in 5 experiments (10 replicate runs each) continuously measuring 137 MRM’s, demonstrating the precision achievable in complex digests. Depletion of 6 high abundance proteins by immunosubtraction significantly improved CV’s compared to whole plasma, but analytes could be detected in both sample types. Replicate digest and depletion/digest runs yielded correlation coefficients (R2) of >99.5% and >98.9% respectively. Absolute analyte specificity for each peptide was demonstrated using MRM-triggered MS/MS scans. Reliable detection of L-selectin (measured at 0.67 ug/ml) and fibronectin indicate that proteins down to the ug/ml level can be quantitated in plasma with minimal sample preparation, yielding a dynamic range of 4.5 orders of magnitude in a single experiment. Peptide MRM measurements in plasma digests thus provide a rapid and specific assay platform for biomarker validation, one which can be extended to lower abundance proteins by enrichment of specific target peptides (SISCAPA).
Revised on November 28, 2005
Accepted on December 6, 2005
Quantitative mass spectrometric MRM assays for major plasma proteins
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