Quantitation tools for stable isotope labelling

[Stortebecker]

Hejhej, I have a question regarding current options in GalaxyP for protein quantitation, especially on stable isotope labels (e.g. SILAC). While there are a lot of good possibilities for peptide identification and protein inference, I do not see many options for quantitation. There is ProteinPilot and Scaffold, but its both not freeware. The integration of MaxQuant was discontinued, as @bgruening told me. I am not sure, if XPRESS and ASAPRatio from the Trans-Proteomic-Pipeline have been integrated, but I would rather not recommend them to anybody. (That's why.)

So the only possibilities I see come from the OpenMS project, e.g. FeatureFinderMultiplex and ERPairFinder. Did I get this correct or am I overlooking quantitation functions of other (free) tools?

[PratikDJagtap]

Hello Florian,

@getiria-onsongo from the Galaxy-P team has been looking at a few quantitation tools (PyQuant, REPORTER, etc.) to be integrated into Galaxy-P. It would be nice to have quantitation tools integrated into Galaxy-P.

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 Mon, Nov 7, 2016 at 2:46 PM, Florian Christoph Sigloch < notifications@github.com> wrote:

Hejhej, I have a question regarding current options in GalaxyP for protein quantitation, especially on stable isotope labels (e.g. SILAC). While there are a lot of good possibilities for peptide identification and protein inference, I do not see many options for quantitation. There is ProteinPilot and Scaffold, but its both not freeware. The integration of MaxQuant was discontinued, as @bgruening https://github.com/bgruening told me. I am not sure, if XPRESS and ASAPRatio from the Trans-Proteomic-Pipeline have been integrated, but I would rather not recommend them to anybody. (That's why. https://www.ncbi.nlm.nih.gov/pubmed/?term=nilse+sigloch)

So the only possibilities I see come from the OpenMS project, e.g. FeatureFinderMultiplex and ERPairFinder. Did I get this correct or am I overlooking quantitation functions of other (free) tools?

— 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/82, or mute the thread https://github.com/notifications/unsubscribe-auth/AKL0OjQnfWrM_i5HEdYwYBmJmRzXtjwDks5q744fgaJpZM4KrsSh .

[glormph]

There is also dinosaur ( https://github.com/fickludd/dinosaur ), but I don’t think there is a Galaxy package for it yet. cheers, — Jorrit Boekel Proteomics systems developer Lehtiö lab / NBIS Scilifelab Stockholm, Sweden

On 07 Nov 2016, at 21:46, Florian Christoph Sigloch notifications@github.com wrote:

Hejhej, I have a question regarding current options in GalaxyP for protein quantitation, especially on stable isotope labels (e.g. SILAC). While there are a lot of good possibilities for peptide identification and protein inference, I do not see many options for quantitation. There is ProteinPilot and Scaffold, but its both not freeware. The integration of MaxQuant was discontinued, as @bgruening told me. I am not sure, if XPRESS and ASAPRatio from the Trans-Proteomic-Pipeline have been integrated, but I would rather not recommend them to anybody. (That's why.)

So the only possibilities I see come from the OpenMS project, e.g. FeatureFinderMultiplex and ERPairFinder. Did I get this correct or am I overlooking quantitation functions of other (free) tools?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[jhervey4]

What instrument vendor are you acquiring data on??

Sipros & ProRata are good combination for ID & quantification: http://sipros.omicsbio.org/ Publication: https://www.ncbi.nlm.nih.gov/pubmed/23793753

ProRata has a great deal of flexibility b/c you can specify elemental compositions between the search ID tool (Sipros) & the quantification configuration. I used this software years ago for 15N labeling of microbes: http://pubs.acs.org/doi/abs/10.1021/pr801088f

As these tools are under development, I am hoping to add them to the Galaxy suite.

Hope this helps!

[bgruening]

@jhervey4 awesome, please let us know if you need any kind of support for getting these tools into Galaxy and join us in https://gitter.im/GalaxyProteomics/Lobby

[bgruening]

@jhervey4 can you join us next Thursday and Friday for a Online Contribution fest? We could work on these tools.

[Stortebecker]

Hejhej, I started making a list of tools that can handle PSM / peptide / protein quants. You are invited to help me complete it.

Based on this list, we can discuss which tool would be the tool-of-choice? For my tutorials, I will start with OpenMS tools for now, as they are already available in Galaxy and can handle anything up to protein quantitation. There are many different quantitation tools in the OpenMS, though, and I will have to work out which one is best for which type of data. Does anyone have experience with these tools?