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© 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 [email protected]
http://sitemaker.umich.edu/iwsmoi
