Final answer:
In Data Dependent Acquisition mode of mass spectrometry, 'most intense peptide ions' refer to the peptide ions with the highest signal intensities selected for subsequent fragmentation and analysis, assisting in protein identification and quantitation.
Step-by-step explanation:
Understanding 'Most Intense Peptide Ions' in DDA mode of Mass Spectrometry
In mass spectrometry, when operated in Data Dependent Acquisition (DDA) mode, the 'most intense peptide ions' refers to the peptide ions that have the highest signal intensity in the initial mass spectrometry (MS) survey scan. These ions are then selected for further fragmentation and analysis. The Orbitrap Elite system might perform an MS survey scan and then isolate and fragment the 15-20 most abundant, multiply-charged precursor ions that exceed a set threshold ion count. These precursor ions are typically the ones that will give the most information about the sample because their abundance signifies a higher presence of the corresponding peptides in the mixture.
For instance, a common method of ion selection for DDA in tandem mass spectrometry involves isolating peptide ions that exceed an intensity threshold, such as the mentioned ion count above 50,000. This selection process aims to maximize the probability of identifying peptides through subsequent tandem MS (MS/MS). Instruments like the LTQ mass analyzer or a high energy collisionally induced dissociation (HCD) mass analyzer are then used to analyze these fragmented ions at a set resolution. After fragmentation, mass spectrometers like the Orbitrap are capable of determining the mass-to-charge ratios (m/z) of the peptide fragments, thereby enabling protein identification and quantitation.