Hi, You could use ProtyQuant, which calculates the 'accumulated peptide presence' for each hypothetical protein:
https://chemrxiv.org/articles/preprint/ProtyQuant_Comparing_Label-Free_Shotgun_Proteomics_Datasets_Using_Accumulated_Peptide_Probabilities/12404363 The algorithm is similar to spectral counting (e.g. used by the StPeter plugin of the TFF), but integrating the protein inference calculation and quantification. The input files are pepXML of the Trans-Proteomic Pipeline. Results are plain text files (tables.) You can find the software at: https://bitbucket.org/lababi/protyquant/ Feedback and questions are welcome (the manuscript is currently under review). Best regards, Robert Excerpts from Mehar Un Nissa's message of 2020-08-25 14:47:34 +0530: > Dear Sir/Madam, > Which tool in TPP is used to get the abundance value or is there any other > way to measure the protein expression? > > I look forward to hearing from you. > > Thanks and regards, > > *Mehar Un Nissa* > Research Scholar, > Proteomics Lab. > Department of Biosciences and Bioengineering, > Indian Institute of Technology, Bombay-400076 > -- 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/1598356573-sup-6526%40rob-Lenovo-Y720-15IKB.
