Supplementary tables
Supplementary Table 1. FAIMS DDA glycopeptide identifications ofN. gonorrhoeae MS11. Combined MSFragger PSM peptide level searches of all potential glycopeptides identified across biological replicates (n=3) are provided. For all identified glycopeptides the spectrum, data files, peptide sequence, peptide length, charge, retention times, observed m/z, calibrated m/z, observed mass, calibrated mass, delta mass, scores, peptide position within protein, assigned modifications, glycan assignment quality, compensation voltage, protein, protein.ID and replicate number are provided. The manually curated glycopeptides spectra used for the creation of the Supplementary Data 1 as well as the localized glycosylation sites and list of all PSM events matching identified curated glycopeptides used for the generation of figures are also provided.
Supplementary Table 2. FAIMS DDA glycopeptide identifications ofN. gonorrhoeae expressing different pglO alleles.Combined MSFragger PSM peptide level searches of all potential glycopeptides identified across pooled references (n=15) are provided. For all identified glycopeptides the spectrum, data files, peptide sequence, peptide length, charge, retention times, observed m/z, calibrated m/z, observed mass, calibrated mass, delta mass, scores, peptide position within protein, assigned modifications, glycan assignment quality, compensation voltage, protein, protein.ID and genotype are provided. The manually curated glycopeptides spectra used for the creation of the Supplementary Data 2 including the localized glycosylation sites and list of all PSM events matching identified curated glycopeptides used for the generation of figures are also provided.
Supplementary table 3. DIA Protein level analysis of N. gonorrhoeae expressing different pglO alleles. The Spectronaut search results for protein level analysis across all biological replicates (n=4), the MaxLFQ Perseus processed data and Z-score Perseus processed data are provided. For each identified protein, the log2 LFQ protein values, T-‑test information including the -log10(p -value), difference in the mean between the groups and if the resulting p -values are below 0.05, the multiple hypothesis corrected p ‑values (permutation-based false discovery rate of 0.05) are provided. Categorical information associated with protein accessions, gene name, and GO terms are provided in addition to if proteins were identified by a single PSM as well as the total number of precursors assigned for each protein within each replicate.
Supplementary table 4. Glycoproteins identified across FAIMS experiments. All proteins identified to be glycosylated within this study and their corresponding NGO assignments are provided.
Supplementary Table 5. Enrichment analysis of global proteome changes in response to N. gonorrhoeae expressing different pglO alleles . Fisher exact tests of proteins determined to undergo statistically significant changes were assessed for co-occurrence of statistically significant changes across strains as well as enrichment of GO terms.
Supplementary table 6. DIA peptide level information of non-glycosylated peptides targeted for glycosylation within the N. gonorrhoeae proteome. The Spectronaut search results for peptides of interest observed across N. gonorrhoeae expressing differentpglO alleles biological replicates (n=4) are provided. For each peptide the protein group, UniProt ID, protein group p-value, Q-value, C-score, Protein Molecular Weight, Proteotypic status of the peptide, Peptide Position, Precursor ID, Precursors Qvalue, Signal To Noise and Total Quantity (ion intensity) are provided.
Supplementary Data 1: Manually curated N. gonorrhoeaeMS11 glycopeptides (Best scoring unique glycopeptides). For each of the best scoring unique glycopeptides, the MSfragger assigned spectra is provided in addition to the assigned Ngo assignment, site, peptide assignment, assignment associated metrics (m/z; observed m/z, score, position in protein) and page within the pdf the HCD and EThcD spectra can be found are provided.
Supplementary Data 2: Manually curated glycopeptides in N. gonorrhoeae expressing different pglO alleles (Best scoring unique glycopeptides). For each of the best scoring unique glycopeptides, the MSfragger assigned spectra is provided in addition to the assigned Ngo assignment, site, peptide assignment, assignment associated metrics (m/z; observed m/z, score, position in protein) and page within the pdf the HCD and EThcD spectra can be found are provided.