Dear Jimmy Thanks for your reply. I will use the correct database.
Felipe El jue, 4 may 2023 a las 15:30, Jimmy Eng (<jke...@gmail.com>) escribió: > Felipe, > > You should not search sequence databases composed of just a single protein > or even tens of proteins and hope to process them through downstream > validation tools like the Prophets. When you do this, you break lots of > assumptions that the tools expect which makes the results, like > probability of 1 for many peptides, meaningless. Ideally you search the > full organism protein sequence database. But if you feel you understand > the analysis and tools well enough that you need to search a smaller > database, minimally use 500 or 1000 protein sequences and include your > protein of interest. > > Jimmy > > On Wed, May 3, 2023 at 9:41 PM felipe velasquez <pipe7...@gmail.com> > wrote: > >> 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 >> <https://groups.google.com/d/msgid/spctools-discuss/CAA35R_USUE5W5p%2BmftygEtM%3Dz-vhHKU0eUuneKZis-w1OxGRng%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/CAJqD6EO48d30S_XX4zLMS3XaEQGrN3h-oRXfe88q4s7UN9vsJQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EO48d30S_XX4zLMS3XaEQGrN3h-oRXfe88q4s7UN9vsJQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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