PIA - Protein Inference Algorithms

[bgruening]

Is this intersting for GalaxyP?
https://github.com/mpc-bioinformatics/pia

[PratikDJagtap]

Hello Bjoern,

While on one side, the feature mentioned below within PIA - would be good
to have - we already have a protein inference algorithm in PeptideShaker.

"... allows you to inspect your peptide spectrum matches, calculate FDR
values across different search engine results and visualize the
correspondence between PSMs, peptides and proteins."

My vote would be to keep it on the watch list but not wrap it now.

Regards,
Pratik

Pratik Jagtap,

Research Assistant Professor, Department of Biochemistry, Molecular Biology
and Biophysics,

University of Minnesota.

Address: 7-166 MCB, 420 Washington Ave SE, Minneapolis, MN 55455

*Phone: 612-624-0381 http://612-624-0381/ Email: pjagtap@umn.edu
pjagtap@umn.edu *

*Twitter: twitter.com/pratikomics http://twitter.com/pratikomics
Google Scholar: z.umn.edu/pjgs http://z.umn.edu/pjgs *

http://z.umn.edu/galaxypreferences

On Wed, Nov 9, 2016 at 5:15 AM, Björn Grüning notifications@github.com
wrote:

Is this intersting for GalaxyP?
https://github.com/mpc-bioinformatics/pia

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[PratikDJagtap]

I would agree on Pratik's comment - interesting but not a high priority
right now. Somewhat redundant with functionality already available in
PeptideShaker, but does have some interesting visualization aspects it
looks like.

• TG

On Wed, Nov 9, 2016 at 7:54 AM, Pratik Jagtap pjagtap@umn.edu wrote:

Hello Bjoern,

While on one side, the feature mentioned below within PIA - would be
good to have - we already have a protein inference algorithm in
PeptideShaker.

"... allows you to inspect your peptide spectrum matches, calculate FDR
values across different search engine results and visualize the
correspondence between PSMs, peptides and proteins."

My vote would be to keep it on the watch list but not wrap it now.

Regards,
Pratik

Pratik Jagtap,

Research Assistant Professor, Department of Biochemistry, Molecular
Biology and Biophysics,

University of Minnesota.

Address: 7-166 MCB, 420 Washington Ave SE, Minneapolis, MN 55455

*Phone: 612-624-0381 http://612-624-0381/ Email: pjagtap@umn.edu
pjagtap@umn.edu *

*Twitter: twitter.com/pratikomics http://twitter.com/pratikomics
Google Scholar: z.umn.edu/pjgs http://z.umn.edu/pjgs *

http://z.umn.edu/galaxypreferences

On Wed, Nov 9, 2016 at 5:15 AM, Björn Grüning notifications@github.com
wrote:

Is this intersting for GalaxyP?
https://github.com/mpc-bioinformatics/pia

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#85, or mute
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Tim Griffin, Ph.D.
Professor, and
Director, Center for Mass Spectrometry and Proteomics
University of Minnesota
Dept. of Biochemistry, Molecular Biology and Biophysics
6-155 Jackson Hall
321 Church Street SE
Minneapolis, MN 55455
USA

Office: 7-144 Molecular Cellular Biology (MCB)

Tel: 612-624-5249
Fax: 612-624-0432
Email: tgriffin@umn.edu

https://www.cbs.umn.edu/bmbb/contacts/timothy-j-griffin
Center for Mass Spectrometry and Proteomics website:
http://www.cbs.umn.edu/msp/