Detection of potential ion suppression for peptide analysis in nanoflow liquid chromatography/mass spectrometry.

A detection technique for ion suppression in liquid chromatography/mass spectrometry (LC/MS) was developed by adding a probe to an LC mobile phase at a certain concentration. The probe is so hydrophilic that it is not adsorbed in a reversed-phase nanoflow LC column, and, furthermore, has an isoelectric point of about 3, which is lower than that for most peptides and is close to the pH of the mobile phase. The intensity of the protonated probe molecule decreases much more than that of other peptides when ion suppression occurs.

'Information-Based-Acquisition' (IBA) technique with an ion-trap/time-of-flight mass spectrometer for high-throughput and reliable protein profiling.

Highly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS). In an LC/MS run, intense peptide ions originating from high-abundance proteins are preferentially analyzed using tandem mass spectrometry (MS(2)), so obtaining the MS(2) spectra of peptide ions from low-abundance proteins is difficult even if such ions are detected. Furthermore, the MS(2) spectra may produce insufficient information to identify the peptides or proteins.