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 [email protected] <[email protected]> > 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 [email protected]. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/spctools-discuss/70df611b-18f3-47b7-860f-e980fd531ea1n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/70df611b-18f3-47b7-860f-e980fd531ea1n%40googlegroups.com?utm_medium=email&utm_source=footer> > > . > > > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/1601903420-sup-6513%40rob-Lenovo-Y720-15IKB.
