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The database searching parameters included up to two missed cleavages allowed for full tryptic digestion, and a precursor ion mass tolerance of 20 ppm.
The applied searching parameters were the same as described above.
The database searching parameters included full tryptic digestion and allowed up to two missed cleavages, precursor mass tolerance 2 Da, and fragment mass tolerance 1 Da.
The in-gel digestion and LC-MS/MS analysis were performed as previously described with exactly the same apparatus, LC separation conditions, and searching parameters [ 25].
To determine the sensitivities of the halogen tags, we found searching parameters for each tag that fixed the maximum number of false positive identifications at 100.
For the mapping of Alu sequences, the human Alu-Sx subfamily consensus sequence [ 15] was matched with the full human genome, using the software BLAST (release 2.2.21, taken from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/) with standard (default) searching parameters.
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The searching parameter was set at twice as default value 16 to ensure the space coverage.
The second procedure is to separate shift parameter searching from angle parameter searching (Fig. 3B).
Database-searching parameters included the following: tryptic digestion with one possible missed cleavage, static modifications for carbamidomethyl (C).
Pay attention to your search parameters so that there are no rude surprises.
Detailed search parameters are printed in the search output XML files.
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