For analysis by MALDI-TOF/TOF, a solution of a-cyano-4hydroxycinnamic acid (matrix, 3 mg) in ethanol:acetone (10 ml, 2:1) was prepared freshly. Samples processed as described above and matrix solution were mixed in a ratio of 1:4, and 1 mL aliquots were spotted in triplicates on an Anchor Chip MALDI plate (Bruker Daltonics, Bremen, Germany). Data was acquired on an UltraFlex MALDI-TOF/TOF instrument (Bruker Daltonics, Bremen, Germany) at 60% laser power until a total intensity of 2610 5 ion counts was reached. Spectra were analyzed using Bruker Daltonics FlexAnalysis software (version 2.4). For LC-MS/ MS tandem mass spectrometry, analysis was carried out by so that the time point when plasma viral RNA was first detected is aligned (vertical line). Post-viremic time points are indicated by the horizontal arrow. (C) A-SAA and C-SAA protein levels in sequential plasma samples from 3 donors acquiring HCV infection (top panel) and 3 donors acquiring HBV infection (bottom panel). As above, the two sets of blots are positioned so that the time point when plasma viral nucleic acids were first detected is aligned (vertical line); and post-viremic time points are indicated by the horizontal arrow. doi:10.1371/journal.ppat.1000893.g003 injection of 3 ml of sample prepared as described above on a nanoAcquity UPLC system coupled to a Waters Q-TOF Premier tandem mass spectrometer in MS E (high/low collision switching) mode as described previously [46] . Processing of raw data was performed using the ProteinLynx Global Server 2.2.5 software and the data were interrogated on an in-house MASCOT server (version 2.2). Alternatively, samples were analyzed on a Bruker HCTplus Ion Trap tandem mass spectrometer (Bruker Daltonics, Bremen, Germany) as described [47] . Semi-quantitative analysis of MS data was based on measuring peak heights observed for the peptide masses that were assigned to A-SAA 86 