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Mass tolerance of parent ion and fragment ion was 1.5 Da and 1.3 Da, respectively.
Searching was performed using a missed cleavage site of one and a peptide mass tolerance of at most ±0.5 Da.
Peptide matching and protein searches against the NCBI nonredundant (nr) databases were performed using the Mascot search engine (http://www.matrixscience.com) with a mass tolerance of ±0.3 Da.
Also in order to reduce the number of possible matches, the nitrogen rule and a mass tolerance of 10 mmu were employed.
The data were searched with a peptide mass tolerance of ±5 ppm and a fragment mass tolerance of ±0.6 Da.
Two missed cleavages per peptide were allowed, and a mass tolerance of 50 ppm was used.
X! Tandem was searched with a fragment ion mass tolerance of 0.60 Da.
Both Sequest and Mascot were set up to search the TAIR8 (200804133024024 entries) database, and both searches were done with a parent ion mass tolerance of 5.0 ppm and a fragment ion mass tolerance of 0.50 Da.
For Orbitrap data, precursor and fragment mass tolerances of 15 ppm and 0.6 Da respectively were allowed, and for QSTAR data a precursor mass tolerance of 100 ppm and fragment mass tolerance of 300 ppm was considered.
The non-redundant sub database of Homo sapiens was used with the parameters as follows: partial oxidation of methionine (+16 Da), and cysteine alkylation (+57 Da), peptide mass tolerance of 1.5 Da and fragment ion mass tolerance of 0.8 Da.
Searches were performed with a fragment ion mass tolerance of 0.8 Da and a parent ion tolerance of 50 ppm.
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