The survey's quality control such as sample size, questionnaire modifications or adjustments, sample random selection has been done by ICT.
Several spots resulted in identical protein identification, presumably due to the formation of protein isoforms bearing various modified residues introduced by post-translational modification or during sample processing.
Some of the conclusions drawn using DSI-ICP-AES are equally valid for DSI-ICP-MS: for example, the effects of cup geometry and composition, drying and charring conditions, carbide formation, the temperature of a graphite cup in a plasma, volatilization enhancement using mixed-gas plasmas and in-situ chemical modification, pre-concentration or sample clean-up and slurry sampling, to name but a few.
Post-translational modifications, low-quality spectra or peptide modifications during sample preparation dramatically complicate the peptide identifications84, 85.
Misidentification of novel histone PTMs can come from a variety of sources including isobaric mass shifts due to histone sequence variation or other modifications, sample preparation, gas phase chemistry within the mass spectrometer, and false positives or incorrect database assignments [ 22].
Amylase activity in the supernatant was measured directly using the Phadebas kit (Magle Life Sciences, Lund, Sweden) according to the manufacturer's procedure, with the following modifications: the sample volume was 0.5 or 0.05 ml and the reactions were conducted at 50°C.
Furthermore, biologically modified peptides may undergo a series of ex vivo modifications during sample preparation which compromise the integrity of the original peptide thus preventing its identification.
Such fortuitous modifications during sample preparation/analysis are the downfall of automated data interpretation.
Samples were assayed in triplicate for these factors following manufacturer's protocols with minor modifications in sample dilutions as necessary.
However, these variants are much like protein modifications, the sample space of which is difficult to estimate explicitly.
