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pmic7474-sup-0001-suppmat.docx20KSupporting Information
pmic7474-sup-0002-figureS1.eps1035KFigure 1. (A) Extracted ion chromatogram (XIC) of the frequently observed HexNAc ion at m/z 204.0866. All the reported scans were detected by PTM MarkerFinder by using the threshold of 2 marker ions required and minimum marker ion relative intensity of 2%. The scans marked with * were not detected since only the marker ion at m/z 204.08665 is present and/or the sum of the marker ion intensities is lower than 2%. The scans marked with # were not detected since the ion m/z 204.08665 ion is an artifact coming from the background noise of the ion at 204.1361 (y2 GK di-peptide), and is filtered out during the mgf processing (i.e. panel B, scan 2042).
pmic7474-sup-0003-tableS1.xlsx13KTable 1. Results of PTM MarkerFinder analysis of a Mascot output file (.dat) containing HCD and ETD spectra from a sample enriched in HexNAc glycopeptides. By using lower intensity thresholds (min relative% ions) and a lower number of marker ions (min # Marker ions), different numbers of putative PTM spectra (pPTM spectra) can be detected. The number of pPTM HCD and ETD spectra that Mascot could identify as glycopeptides are reported.
pmic7474-sup-0004-tableS2.xlsx15KTable 2. Results of PTM MarkerFinder screening of HCD spectra from a tryptic digest of yeast proteins analyzed by LC-MS/MS. The spectra have been searched for HexNAc (N), Hex (S,T), methyl (K,R), dimethyl (K,R) and acetyl (K) using Mascot. For every modification, a different minimum number of required marker ions (min # Marker ions) and marker ion intensity threshold (min relative% ions) were set. The number of putative PTM spectra (pPTM spectra) are reported. The number of pPTM spectra that Mascot could identify with low (score <20, Exp. value >0.05, “low conf.”) or high (score >20, Exp. value <0.05, “high conf.”) confidence are shown. The values were selected arbitrarily as threshold for correct peptide sequence identification. The list of marker ions is defined as in reference [1] (Matthiesen et al., J. Proteome Res. 2005, 4(6):2338–47.), except for the modifications HexNAc and Hex (described in the manuscript) and “glycan signatures” (m/z 366.1400 (Hex-HexNAc+), 325.1135 (Hex-Hex+), 274.0927 (NeuAc+-H2O), 204.0866 (HexNAc+), 163.0601 (Hex+)

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