Re: [spctools-discuss] LFQ

[Robert Winkler]

For LFQ and sample comparison, you also could try ProtyQuant, which uses
TPP pepXML (PeptideProphet validated) as input.
https://www.sciencedirect.com/science/article/pii/S1874391920303535
Best, Robert

Excerpts from 'Luis Mendoza' via spctools-discuss's message of 2020-10-02 
13:07:24 -0700:
> The other alternative is to run XPRESS in Label-free mode.  For peaks where
> it can extract intensities, it will report two results: one for the
> integrated area with corresponding scan range, and one for the maximum peak
> intensity along with the scan number of that peak.  You can view and export
> these values in the PepXMLViewer.  Unfortunately, they cannot be used for
> quantitation of proteins within TPP tools.
> 
> If you are looking to quantify proteins, we do recommend that you give
> StPeter a try.  Its main algorithm is based of fragment ion intensities
> from corresponding PSMs, although it can also report a value based on
> spectral counting.
> 
> Hope this helps.
> --Luis
> 
> On Fri, Oct 2, 2020 at 12:06 AM vipulb...@gmail.com 
> wrote:
> 
> > I am a using  TPP v5.2.0 Flammagenitus  to analyze label free data
> > generated on a Thermo QExactive machine. I  want to perform LFQ, is there
> > anyway to get Intensity values from the TPP. I am not sure about using
> > StPeter since it is based on spectral counting. How can I perform LFQ in
> > TPP ?
> >
> > --
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> > 
> > .
> >
> 

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Re: [spctools-discuss] LFQ

['Luis Mendoza' via spctools-discuss]

The other alternative is to run XPRESS in Label-free mode.  For peaks where
it can extract intensities, it will report two results: one for the
integrated area with corresponding scan range, and one for the maximum peak
intensity along with the scan number of that peak.  You can view and export
these values in the PepXMLViewer.  Unfortunately, they cannot be used for
quantitation of proteins within TPP tools.

If you are looking to quantify proteins, we do recommend that you give
StPeter a try.  Its main algorithm is based of fragment ion intensities
from corresponding PSMs, although it can also report a value based on
spectral counting.

Hope this helps.
--Luis

On Fri, Oct 2, 2020 at 12:06 AM vipulb...@gmail.com 
wrote:

> I am a using  TPP v5.2.0 Flammagenitus  to analyze label free data
> generated on a Thermo QExactive machine. I  want to perform LFQ, is there
> anyway to get Intensity values from the TPP. I am not sure about using
> StPeter since it is based on spectral counting. How can I perform LFQ in
> TPP ?
>
> --
> 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-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/70df611b-18f3-47b7-860f-e980fd531ea1n%40googlegroups.com
> 
> .
>

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