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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/galaxyproteomics/tools-galaxyp/issues/85, or mute the thread https://github.com/notifications/unsubscribe-auth/AKL0OpnsHPhY7bXIWME31eDIvdUVLDJgks5q8atugaJpZM4KtbA1 .

[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 https://github.com/galaxyproteomics/tools-galaxyp/issues/85, or mute the thread https://github.com/notifications/unsubscribe-auth/AKL0OpnsHPhY7bXIWME31eDIvdUVLDJgks5q8atugaJpZM4KtbA1 .

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/