<p>Excitation-emission matrix (EEM) fluorescence spectroscopy has been widely used to characterize chemical components of brown carbon (BrC), yet the molecular basics and formation mechanisms of chromophores decomposed by parallel factor (PARAFAC) analysis are not fully understood. Here, water-soluble organic carbon (WSOC) in aerosols from Karachi, Pakistan, were characterized with EEM spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Three PARAFAC components were identified, including two humic-like (C1 and C2), and one protein-like (C3) species. Among them, the C2 shows the longest emission maxima (~494 nm), and correlates tightly with the mass absorption efficiency at 365 nm (MAE₃₆₅), the character of BrC. Molecular families associated with each of the three components were determined by Spearman correlation analysis between FT-ICR MS peaks and PARAFAC component intensities. The C1 and C2 components are associated with nitrogen-enriched compounds, despite that C2 more with higher aromaticity, higher N content, and highly oxygenated compounds. The formulas associated with C3 include fewer nitrogen-containing species, with a lower unsaturated degree and oxidation state. A dominant oxidation pathway for the formation of C1 and C2 components was suggested, notwithstanding their different precursor types. A large number of formulas associated with C2 were found to be located in the &ldquo;potential BrC&rdquo; region, overlapped with BrC-associated formulas, and readily correlated tightly with MAE₃₆₅. This suggests that the compounds illuminating C2 may have also contributed substantially to the BrC light absorption. These findings were important for future studies using the EEM-PARAFAC method to explore the compositions, processes, and sources of atmospheric BrC.</p>