improving peptide probability modeling in scaffold 4

Improving Peptide Probability Modeling in Scaffold 4

Brian C. Searlebrian.searle@proteomesoftware.com

Scaffold Users Meeting, 2013

Creative Commons Attribution

Scaffold 4 Improvements

• Probability Estimation using LFDR

• Target/Decoy Classification of multiple scores

• Delta Mass Error Modeling Improvements

• Requires Target/Decoy analysis (1:1 … 1:10)

“Correct”

“Incorrect”

p( | D) p(D | ) p()

p(D | ) p() p(D | ) p( )

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

XCorr

DeltaCN

% Ions Identified

…

XCorr

DeltaCN

% Ions Identified

…

XCorr

DeltaCN

% Ions Identified

€

discriminant score = logp(D | +)∏p(D | −)∏

⎛

⎝ ⎜ ⎜

⎞

⎠ ⎟ ⎟

Naïve Bayes Classifier

• Trained to each data set

• Simple (can calculate with a formula, no magic!)

• Robust to over-fitting

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

Probability the ID is Correct

Probability the ID is Wrong

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

Protein-Level False Discovery Rate

Num

ber o

f Ide

ntifi

ed P

rote

ins

Num

ber o

f Ide

ntifi

ed P

rote

ins

1% Peptide FDR

Num

ber o

f Ide

ntifi

ed P

rote

ins

Protein-Level FDR

1% Peptide FDR > 10% Protein FDR?!?

New Search Engines?

• Difficult to add new search engines with PeptideProphet (new seeds)

• Easy to add with Naïve Bayes / LFDR

• mzIdentML interchange (HUPO standard)

New Search Enginesin Scaffold 4

• Peaks• Byonic• Myrimatch (Tabb Lab)• SQID (Wysocki Lab)• MS-GF+ (Pevzner Lab)• MS-Amanda (Mechtler Lab, PD)

New Search Enginesin Scaffold 4

• Peaks• Byonic• Myrimatch (Tabb Lab)• SQID (Wysocki Lab)• MS-GF+ (Pevzner Lab)• MS-Amanda (Mechtler Lab, PD)

• ... Any engine with decoys & mzIdentML!

Scaffold 4 Improvements

• New Naïve Bayes / LFDR Probabilities– Probability Estimation using LFDR– Target/Decoy Classification– Delta Mass Error Modeling– “Next generation” search engine interpretation

• New mzIdentML File Loading– Several newly supported search engines– Any search engine with decoys