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ptm-analysis

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Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with MSstatsPTM - plus kinase-activity and functional triage. Covers MaxQuant Phospho (STY)Sites multiplicity expansion, localization-probability filtering (class I, Ascore, ptmRS, DIA EG.PTMLocalizationProbabilities, DIA-NN PTM.Site.Confidence), false localization rate (LuciPHOr/DeepFLR), motif analysis with experiment-matched backgrounds, diGly/K-GG ubiquitin specificity, acetyl/glyco traps, and KSEA/PTM-SEA. Use when localizing and quantifying phosphorylation, acetylation, ubiquitination, or glycosylation sites from enrichment-based runs and deciding whether an apparent site change is real after subtracting protein abundance. Peptide ID and open/variable-mod search is peptide-identification; underlying protein-level quant is quantification and differential-abundance; DIA acquisition mechanics is dia-…

When to use

• localizing and quantifying phosphorylation, acetylation, ubiquitination, or glycosylation sites
• deciding whether an apparent site change is real after subtracting protein abundance
• MaxQuant Phospho (STY)Sites multiplicity expansion
• localization-probability filtering
• false localization rate (LuciPHOr/DeepFLR)
• motif analysis with experiment-matched backgrounds
• diGly/K-GG ubiquitin specificity
• KSEA/PTM-SEA

When not to use

• peptide ID and open/variable-mod search
• underlying protein-level quant
• DIA acquisition mechanics
• intact-glycopeptide glycan-composition search
• absolute occupancy from three-ratio SILAC

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