© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

Hands-On Tutorial Using ProTIP

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

Performing search through ProTIP.

•  Loading datasets •  Sharing datasets •  Setting up an OMSSA search •  Setting up Scaffold Analysis through ProTIP •  Scaffold analysis •  Benefits of Combining results through Scaffold.

© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

Mass spectral search algorithms match experimental spectra (peaklists) against theoretical spectra (FASTA) - on a global scale.

Protein Peptide

Mass spectrum

Fragmentation

Search against database.

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

mass spectrum In

tens

ity

Mass / charge

© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

Mass Spectrometers & data formats

Thermofinnigan Xcalibur / .raw Life Technologies Analyst / .wiff ; .t2d

Waters Masslynx / .raw Bruker .baf

Mascot

Sequest

X! tandem OMSSA

ProteinPilot

© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

search algorithm

   Mass Spectrometry 

Mass spectral data. 

Search algorithm 

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

search algorithms

   Mass Spectrometry 

Mass spectral data. 

Search algorithm 

Sequest 

X!tandem 

OMSSA 

MaxQuant  RDC : sdvlapp32

ProteinPilot  CPC9 ; CGL 138.

Mascot  https://sequest7.msi.umn.edu/mascot

© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

Sta>s>cal valida>on of pep>de and protein iden>fica>ons. 

© 2009 Regents of the University of Minnesota. All rights reserved.

Supercomputing Institute for Advanced Computational Research

Scaffold

Sta>s>cal valida>on of pep>de and protein iden>fica>ons. 

https://www.msi.umn.edu/sw/scaffold-for-pro

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

Raw Data from

Orbitrap mzxml format

dta format

X!TANDEM search

Scaffold Analysis

Scaffold Viewer

ProTIP Workflow

MASCOT search

SEQUEST search

Mgf format

OMSSA search

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

Performing Multiple searches through ProTIP.

# of

pep

tides

# of

pro

tein

s

TEST DATASET

9.5 %

7.5 %

16.4 %

11.9 %

19.4 %

14.6 %

29.5 %

18.4 %

Supercomputing Institute for Advanced Computational Research

© 2009 Regents of the University of Minnesota. All rights reserved.

The University of Minnesota is an equal opportunity educator and employer. This PowerPoint is available in alternative formats upon request. Direct requests to Minnesota Supercomputing Institute, 599 Walter library, 117 Pleasant St. SE, Minneapolis, Minnesota, 55455, 612-624-0528.

LAST WORD…

Questions ? Pratik Jagtap pratik@msi.umn.edu

http://sitemaker.umich.edu/iwsmoi