Download Untitled - GeneBio

submission
•
Yes: Phenyx can distinguish all possible matches and decide which
is/are the most probable.
•
No: Phenyx simply reports all sequences matching with an
acceptable score. Then when the results are available, you deal
personally with any questionable spectra having multiple matches.
Parent Error Tolerance: There are invariably mistakes or
uncontrollable factors that affect measurements. You can allow a certain
amount of deviation between the experimental (observed) parent ion
masses and the theoretical (calculated) masses. Input the value and
choose the corresponding unit in Daltons (Da) or parts per million
(ppm).
Acceptance parameters
Click on the red arrow to view or edit all the acceptance parameters.
Minimum Peptide Length: Peptides with less than the specified
number of amino acids are reported in the peptide match results but
they do not contribute to the protein score. They are labeled as invalid.
Minimum Peptide z-Score: Otherwise known as the peptide or match
score. The distribution of calculated scores is compared to that of
random peptide sequences in order to find the mean and variance. The
z-Score is then a measure of how far and in what direction the score
deviates from the distribution's mean.
Maximum Peptide p-Value: The probability of a peptide match in a
database occurring by chance with this score or better. A p-Value has a
maximum of 1.0. Default score is set to 1e-05. The lower the p-Value,
the more significant the match.
AC Score: Minimum significant value for a protein’s accession number
score. The AC score is the sum of the best scores for validated peptide
sequences. Protein matches scoring lower than this value are rejected
from the identified proteins. (Valid peptides from rejected proteins are
however also listed in the Compounds Overview page, but AC column is
then empty).
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Phenyx Web Interface Manual