Poor scoring … 2.1. Investigation of Selleckchem Bortezomib Sialylated Structures in Human Synovial Lubricin Negative ion LC-MS2 has been

shown to provide detailed structural information of neutral oligosaccharides [8], but it has been suggested that linkage specific sialidases should be used to increase the information about sialylated oligosaccharides [18], where their MS2 spectra is less informative. The sequence and configuration of sialylated structures were addressed using human synovial lubricin Inhibitors,research,lifescience,medical oligosaccharides. The human synovial lubricin was isolated by SDS-PAGE (Figure 2a) and the oligosaccharides from the dominating band in the gel (227-345 kDa) were released by reductive β-elimination [8]. The coomassie stained gel also highlighted two additional bands in the regions of

200 kDa and 65 kDa. The band around 200 kDa regions was found to be fibronectin while the band at 65 kDa region was C terminus of lubricin Inhibitors,research,lifescience,medical when analyzed by proteomic means. These results have been published previously [19]. The spectra of the released oligosaccharides were dominated Inhibitors,research,lifescience,medical by mono- and di-sialylated structures when analyzed by LC-MS2. The assignment of the sialylated structures i.e. [M - H]- ions at m/z 1331 (NeuAc2Hex2HexNAc1HexNAcol) and m/z 1040 (NeuAc1Hex2HexNAc1HexNAcol) gave indecisive scoring (R2) about the sequence of the structures (Table 1) when their MS2 spectral intensities were compared with spectra reported in the MS2 Inhibitors,research,lifescience,medical database UniCarb-DB [16]. The reason was that the sialylated

structures gave similar R2 value between 1st and 2nd ranked structure as shown in Table 1. In addition, the MS2 spectra of the sialylated structures are less informative due to loss of labile sialic acid, which also made their assignment difficult. The less informative MS2 spectrum of the sialylated structures may also be the reason why they are not well assigned by spectral match. Inhibitors,research,lifescience,medical The table also shows the additional data from samples analyzed in this report. Overall it was indicated that neutral structures scored better than sialylated. This is illustrated by the differences in score between the best assigned as 1st ranked (highest R2 value close to 1) and 2nd ranked structure because (2nd highest R2). Therefore, it was concluded that once the sialic acid is removed by sialidase treatment, the remaining structure could be easily assigned by spectral matching. These data suggest that the quality of the spectra from sialylated structures only have limited information about the sequence beside the presence of terminal sialic acid. Figure 2 Negative ion LC-MS2 analysis of sialylated structures in human synovial lubricin. (a) Enrichment of human synovial lubricin by SDS-PAGE. (b) Selected ion chromatogram (SIC) of the [M - H]- ions at m/z 749, 1040 and 1331 before (front) and after the treatment … Table 1 The MS2 spectral intensity correlation comparison of the sialylated and neutral structures with spectra reported in the MS2 database UniCarb-DB.