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.
