Aggrecan is the prominent proteoglycan in cartilage and is modified with approximately 100 chondroitin sulfate (CS) chains through a tetrasaccharide linkage structure. In osteoarthritis (OA), the viscoelastic properties of cartilage are compromised on both the quantity and integrity of aggrecan core protein expressed as well as reduced overall CS chain length. Herein, we postulated that chronic low-level inflammation may also contribute to OA progression by promoting regulatory mechanisms in early CS biosynthesis that yield incomplete linkage structures on aggrecan. To test this idea, chondrocytes extracted from human tali were cultured in alginate beads and challenged with 5 ng/mL IL-1β as a model for chronic inflammation leading to OA progression. Novel mass spectrometry-based methods were devised to detect and quantify partially elongated linkage structures relative to control cultures. The total mole fraction of unelongated xylose residues per aggrecan was significantly less (p = 0.03) after IL-1β treatment compared to control cultures, with unelongated xylose residues constituting between 6% and 12% of the fraction of total CS measured. A portion (<1%) of the partially elongated linkage structures was found to be either phosphorylated or sulfated. These results establish quantitative mass spectrometry as a very sensitive and effective platform for evaluating truncated proteoglycan linkage structures. Our observations using this method suggest a possible role for aberrant linkage structure elongation in OA progression.