A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H 3 PO 4 ) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation. (J Am Soc Mass Spectrom 2002, 13, 792-803)

Di-to heptasaccharides isolated from total nondialyzable brain glycopeptides after release by alkaline borohydride treatment have been subjected to mass spectrometric and nuclear magnetic resonance spectroscopic analyses supplemented by TLC-MS analyses of derived neoglycolipids. A family of Manol-terminating oligosaccharides has been revealed which includes novel sequences with a 2,6-disubstituted Manol:In contrast to the Manol-terminating HNK-1 antigen-positive chains described previously that occur as a minor population [Yuen, C.-T., Chai, W., Loveless, R.W., Lawson, A.M., Margolis, R.U. & Feizi, T. (1997) J. Biol. Chem. 272, 8924±8931], the above oligosaccharides are abundant. The ratio of these compounds to the classical N-acetylgalactosaminitol-terminating oligosaccharides is about 1 : 3. Thus, there appears to be in higher eukaryotes a major alternative pathway related to the yeast-type protein O-mannosylation, the enzymatic basis and functional importance of which now require investigation.Keywords: brain glycoproteins; O-linked glycans; Manol-terminating oligosaccharides; neoglycolipids; TLC/MS.In an earlier study aimed at characterizing O-glycans on glycopeptides from brain that express the sulfoglucuronyl antigen, HNK-1, oligosaccharides were released by reductive alkaline hydrolysis and their immunoreactivities evaluated by the neoglycolipid technology [1]. The immunoreactive oligosaccharides were isolated and found to be tetra-to octasaccharides with the predicted 3-sulfoglucuronyl capping moieties and lactosaminyl backbones; the unexpected finding was that they terminate with hexitol (2-substituted and 2,6-disubstituted) rather than N-acetylgalactosaminitol. In a tetrasaccharide investigated in the greatest detail, the hexitol was identified as 2-substituted Manol [1]. The HNK-1-immunoreactive oligosaccharide alditols were extremely minor components each representing less than 0.1% of the total released oligosaccharides. However, an additional array of more abundant Manol-terminating oligosaccharides was noted including

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Six patients with disorders of peroxisomal function have been studied. Two presented in the neonatal period with the classical features of the Zellweger syndrome, two had incomplete Zellweger phenotypes, one infantile Refsum's disease and one rhizomelic chondrodysplasia punctata. Plasma bile acid profiles were determined using capillary gas chromatography-mass spectrometry. In all patients, except the case of chondrodysplasia punctata, 27-carbon and 29-carbon bile acids were present. The compounds identified included trihydroxycoprostanic acid (THCA), dihydroxycoprostanic acid (DHCA), C24-, C25- and C26-hydroxylated derivatives of THCA, a 27-carbon acid with four nuclear hydroxy groups and 3 alpha,7 alpha,12 alpha-trihydroxy-27a,27b-dihomo-5 beta-cholestan-26, 27b-dioic acid (C29-dicarboxylic acid). THCA was present at a low concentration in the patient with infantile Refsum's disease; the concentration of DHCA and the C29 dicarboxylic acid were considerably higher. The presence of abnormal bile acids in patients with Zellweger syndrome and infantile Refsum's disease could be explained by the absence of peroxisomes from their hepatocytes. In chondrodysplasia punctata the cause of peroxisomal dysfunction must be different, since normal bile acid synthesis is preserved.