Hello Luis Thanks for your request. Yes, I performed TPP/Prophets, and their probability is high as 0.99999 or 1, in many peptides. The database I used only contains my protein of interest in FASTA. I do not know how to use decoys.
Kind regards, Felipe El mar, 2 may 2023 a las 22:53, 'Luis Mendoza' via spctools-discuss (< spctools-discuss@googlegroups.com>) escribió: > Hello Felipe, > > There may be several reasons why you see the viral protein in your > analysis, e.g. > > - Did you only run Comet, or did you validate using the TPP/Prophets? > If the latter, what was the probability of the protein(s) in question? > - What were the contents of the database that you used to search? Did > they contain only "the sequence of my protein of interest"/virus protein, > or did you use a full proteome database? Did you use decoys? > Contaminants? > - Does the virus protein contain peptides that may be shared with > proteins in the sample itself? Do you observe unique/proteotypic peptides > from that protein? > > Cheers, > --Luis > > > > On Sun, Apr 30, 2023 at 7:13 PM felipe velasquez <pipe7...@gmail.com> > wrote: > >> Hello >> >> I have a question about protein validation. I am trying to use TPP to >> identify post-translational modifications of certain proteins. I performed >> a Comet search using the sequence of my protein of interest. However, while >> exploring another database, I performed a search using a protein that is >> not in the experimental design, as it comes from a virus. Surprisingly, >> this protein appeared in my analysis. Is this normal? >> >> thanks, >> >> Felipe Ignacio Velásquez Salinas >> Bioquímico >> Doctor en Microbiología >> >> -- >> 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/CAA35R_VO9uJbjkdKoJKrZVFtRnuV04Hp%2B8FMzE1BqaiTYtmx8Q%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAA35R_VO9uJbjkdKoJKrZVFtRnuV04Hp%2B8FMzE1BqaiTYtmx8Q%40mail.gmail.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 spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CACyS9boNhRq47qwaBeQQAdH_N8XwzaBPZOb7cCz7q_TAmmwYag%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CACyS9boNhRq47qwaBeQQAdH_N8XwzaBPZOb7cCz7q_TAmmwYag%40mail.gmail.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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAA35R_USUE5W5p%2BmftygEtM%3Dz-vhHKU0eUuneKZis-w1OxGRng%40mail.gmail.com.
