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.