Chromatography of synovial fluid and fibrinogen-derived peptides. Panel A contains a base peak chromatogram of the LC-MS/MS analysis of the peptides in the synovial fluid of rheumatoid arthritis (RA) patient S13, showing the complexity of the sample. All base peaks derived from the alpha chain of fibrinogen are indicated with 'F', with citrullinated and phosphorylated peptides indicated with 'cF' and 'pF', respectively. Panel B shows the extracted ion chromatograms (XIC) of peptide DSGEGDFLAEGGGVR (mass-to-charge ratio (m/z) 733.33), which elutes at a retention time (RT) of 53.18 minutes and the citrullinated version of the same peptide (m/z 733.83), eluting at 61.08 minutes. Note that in the bottom chromatogram also a peak is visible at the elution time of the noncitrullinated peptide, corresponding to the 13C isotopic peak of that peptide, which has a mass very close to the citrullinated peptide and is, therefore, also extracted by the algorithm. The relative areas of the two extracted chromatograms are indicated at the y-axis of the XICs. LC-MS/MS, liquid chromatography-tandem mass spectrometry.