Data Dependent Acquisition proteomics
Peak lists were generated from DDA raw data with DataAnalysis 4.4
(Bruker Daltonics) and peptide to spectrum matches identified with PEAKS
suite X plus (Bioinformatics Solutions Inc., Waterloo, Canada) and
X!Tandem Alanine (The GPM) database search engines followed by
unambiguous assignment of peptides to unique proteins using the O.
niloticus proteome database downloaded from NCBI RefSeq on Feb. 25,
2020 , supplemented with known O. mossambicus protein sequences.
The search database included 61,681 proteins and an equal number of
randomly scrambled decoys along with 282 common contaminants (human
keratins, porcine trypsin, etc.). Trypsin cleavage was specified at the
C-terminus of Lysine or Arginine except when followed by Proline, and a
maximum of two missed cleavages were allowed. Possible PTMs were
searched by allowing for Cysteine carbamidomethylation, Methionine
oxidation, and Protein N-terminal acetylation. Additionally,
second-round searches considered all 313 PEAKSPTM modifications included
in the default PEAKS suite X plus database, allowing max. 3 PTMs per
peptide. Mass tolerance limits were set at 10 ppm for precursors and
0.03 Da for fragment ions. All DDA data and metadata are available at
MassIVE (MSV000085745) and ProteomeXchange (PXD020364).