StPeter documentation

[Brian Hampton]

Hello,

I would be appreciative if someone could point me to documentation that describes StPeter which is used for label-free quantification in TPP. I've tried the usual searching with Google, PubMed and looking through the SPC Tools sites without success.

Thanks,

Brian

[Jason Winget]

Hi Brian,

StPeter is a direct implementation of the Normalized Spectral Index, described by Griffin et. al: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805705/

It uses MS2 intensities for protein-level quantification.

We are working on publishing it independently but so far journal editors have not been very receptive...

As for usage, if you run StPeter from the command line with no arguments you will see a usage statement. By default it uses only non-degenerate peptides and a 1% FDR cutoff. Typically the default values are fine, so you should just be able to run it against your ProtXML results. It will write the quantification values back into the ProtXML and will also output some simple CSV results.

At the moment PTMs are hard-coded and contain only a limited set, so the most common issue that I run into is that the program will crash when searching "unusual" mods.

-Jason

[Hampton, Brian]

Thanks Jason!  Once your manuscript is published it would be great to announce that on this list. 

Cheers!

Brian

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.

[Filippo GENOVESE]

Any news?

Filippo

To post to this group, send email to spctool...@googlegroups.com.

[Jason Winget]

The manuscript is currently in the reviewer revision stage. Stay tuned, hopefully it will be published in the near future!

[Michael Hoopmann]

Manuscript is in review, but documentation is already under construction: http://tools.proteomecenter.org/wiki/index.php?title=Software:StPeter

Cheers,

Mike

 

To post to this group, send email to spctools...@googlegroups.com.

[Filippo GENOVESE]

Thanks guys.

Could you please briefly comment on how to interpret the StPeter Sin value? The lower, the more abundant or the other way around?

 

Have a nice day

 

Filippo

 

Da: Michael Hoopmann
Inviato: giovedì 14 dicembre 2017 21:15
A: spctools...@googlegroups.com
Oggetto: RE: [spctools-discuss] Re: StPeter documentation

--
You received this message because you are subscribed to a topic in the Google Groups "spctools-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/spctools-discuss/-36bVjElNMo/unsubscribe.
To unsubscribe from this group and all its topics, send an email to spctools-discu...@googlegroups.com.

[Jason]

The negative values tend to throw folks off. The greater the value, the greater the abundance (e. g. -10 > -12). I find it helps to scale all the values by the minimum, shifting them all to positive when presenting the results to others. 

On Dec 15, 2017 9:38 AM, "Filippo GENOVESE" <fgen...@unimore.it> wrote:

Thanks guys.

Could you please briefly comment on how to interpret the StPeter Sin value? The lower, the more abundant or the other way around?

 

Have a nice day

 

Filippo

 

Da: Michael Hoopmann
Inviato: giovedì 14 dicembre 2017 21:15

A: spctools-discuss@googlegroups.com

To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.

Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to a topic in the Google Groups "spctools-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/spctools-discuss/-36bVjElNMo/unsubscribe.

To unsubscribe from this group and all its topics, send an email to spctools-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.

Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to a topic in the Google Groups "spctools-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/spctools-discuss/-36bVjElNMo/unsubscribe.

To unsubscribe from this group and all its topics, send an email to spctools-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.

[Michael Hoopmann]

Here is the publication: https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00786