Supplementary Figure 12: Accounting for ontologies enriched among post-isolation modifications.
From: TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets
Gene ontology enrichment analyses of PTM-bearing proteins may be biased by mass spectrometers’ tendency towards identifying modified peptides from highly abundant proteins. Consequently, some ontologies could reach statistical significance based on protein abundance alone, rather than PTM-specific biological phenomena. To account for this, we identified significantly enriched ontologies (1% FDR, Benjamini-Hochberg corrected; yellow) among proteins bearing any of 15 abundant post-isolation modifications. Because these modifications should not have any inherent biological relevance, any ontology enriched among these post-isolation modifications were deemed false (red brackets), and removed from the analysis presented in Fig. 4b.
