I'm using a windows install of TPP, and I'm trying to convert a 250MB
mascot.dat file to pepxml. It works in a reasonable amount of time if I
enable the option 'Use short protein id as per Mascot result (instead of
full protein ids in fasta file)' however if I do tick it, it seems to take
much, much longer. This is the log:
filepath: c:/Inetpub/wwwroot/ISB/data/, extn: F008646
A stored as 71.0371
B stored as 114.535
C stored as 160.031
D stored as 115.027
E stored as 129.043
F stored as 147.068
G stored as 57.0215
H stored as 137.059
I stored as 113.084
J stored as 113.084
K stored as 128.095
L stored as 113.084
M stored as 131.04
N stored as 114.043
O stored as 237.148
P stored as 97.0528
Q stored as 128.059
R stored as 156.101
S stored as 87.032
T stored as 101.048
U stored as 150.954
V stored as 99.0684
W stored as 186.079
X stored as 111
Y stored as 163.063
Z stored as 128.551
c stored as 17.0027
n stored as 1.00783
variable modification 1, delta mass 15.9949 for Oxidation (M):
residues: M
nterm: 0
cterm: 0
protterm: 0
Unknown file type. No file loaded.
warning: cannot open "" for reading scan numbers.
trypsin : cut(KR) nocuts(P) sense(C)
prev_aa and next_aa have already been read from .dat file.
Replacing 304658 protein id with full ids by parsing through the database...
searching c:/Inetpub/wwwroot/ISB/data/nr/nr/nr.fasta.....
It has been going for a few days - is it normal for it to take so long? Is
there any way to speed it up?
I imagine the main factor causing it to go slowly is that it's pulling
details from the huge nr database, which I have in in fasta format. Does
mascot support any kind of indexed files for the databse input file, and
would they be faster?
Thanks for your help!
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