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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
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Enter Scaffold PTM
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Motif Scores
• N = # modified sites in data set• n = # AA combo in data set• p = prior (percentage of AA combo in FASTA)
p valueaa N
k
kn
N
pk (1 p)N k
MotifScore 10 log10(p valueaa )Schwartz D, and Gygi SP 2005 (doi:10.1038/nbt1146)
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Adding Motifs By Hand
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Adding Motifs By Hand
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Adding Motifs By Hand
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Adding Motifs By Hand
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Adding Motifs By Hand
Page 25
ScaffoldQuantML Report
Page 29
Localization Filtering
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Localization Threshold
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Localization Threshold
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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