scaffold ptm 2.0

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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. - PowerPoint PPT Presentation

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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 N

k

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