Sorry if this is covered somewhere else, I was unable to find the answer to this question.
I am using TPP with SEQUEST to search for peptides in mass spectra. I had an original fastafile (specified in the parameters file by "database_name=") that I have been using for all my database_search runs. I just generated a new fasta file that included the possibility of amino acids being cut off the N-terminus of the protein fragments. E.G. If the original fasta file contained MVMNDANQAQITATFKTK The new fasta file contains MVMNDANQAQITATFKTK VMNDANQAQITATFKTK MNDANQAQITATFKTK NDANQAQITATFKTK DANQAQITATFKTK ANQAQITATFKTK NQAQITATFKTK QAQITATFKTK AQITATFKTK These sequences were included because I was concerned that the database_search would not find proteins where the N-terminus was modified. (My work mainly concerns the N-termini of proteins). I ran some preliminary tests to see how this would affect the run speed and results. Using the original fasta file, a run took 3.5 hours. Using the new longer fasta file (which has all the sequences of the original file and more), the same run took 2 hours. There were about 6000 peptides found when run with the original fasta file and only about 2500 peptides found when run with the new longer fasta file. Using the new fasta file, I found some peptide matches with probability of 1 that had slightly lower probability (around 0.9) when using the original fasta file. MY QUESTIONS: Does using a longer fasta file somehow cause a lose of precision when searching for peptide matches in mass spec data? How does the fasta file length (and specifically adding the same sequences with a shortened N-terminus) affect the database_searches and more importantly the peptide matches output? Thank, Kris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
