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Scaffold PTM 2.0
• Brief intro to Scaffold PTM
• What’s new in 2.0!– Global motif analysis (known/unknown)– Quantification at modification sites– Localization filtering
y1 – y5 b12 – b16
Enter Scaffold PTM
Motifs
Motif View
Motif View
Motif View
Motif View
Motif View
Motif View
Motif Scores
Motif Scores
• N = # modified sites in data set• n = # AA combo in data set• p = prior (percentage of AA combo in FASTA)
p valueaa Nk
kn
N
pk (1 p)N k
MotifScore 10 log10(p valueaa )Schwartz D, and Gygi SP 2005 (doi:10.1038/nbt1146)
Adding Motifs By Hand
Adding Motifs By Hand
Adding Motifs By Hand
Adding Motifs By Hand
Adding Motifs By Hand
Quantify
Quantify View
Quantify View
ScaffoldQuantML Report
Quantify View
Quantify View
Quantify View
Localization Filtering
Localization Threshold
Localization Threshold
Scaffold PTM 2.0
• What’s new in 2.0!– Global motif analysis (known/unknown)– Quantification at modification sites– Localization filtering– Loads of bug fixes and minor enhancements
