'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.

Orthogonal trap time-of-flight mass spectrometer using a collisional damping chamber.

We report a new hybrid mass spectrometer, which is a combination of a quadrupole ion trap and an orthogonal time-of-flight (TOF) mass spectrometer. This new configuration consists of a collisional-damping chamber (CDC) inserted between an MSn-capable ion trap and a high-mass-accuracy orthogonal-TOF mass spectrometer. Because the CDC converted an ion packet into an energy-focused and quasi-continuous beam, a high mass resolution of over 10,000 and a high mass accuracy of better than 3 ppm were achieved.

Assignment and quantification of 2-aminopyridine derivatized oligosaccharide isomers coeluted on reversed-phase HPLC/MS by MSn spectral library.

2-Aminopyridine (PA)-derivatized oligosaccharides from IgG were analyzed by using reversed-phase HPLC/mass spectrometry (RP-HPLC/MS) and a MS(n) spectral library, in particular, focusing on two pairs of isomers incompletely separated or coeluted in chromatograms. We previously reported that MS(n) spectral matching considering both major fragment ions (m/z) and intensities is useful and applicable to the structural assignment of PA-oligosaccharide isomers. In this study, MS(n) spectral matching based on the MS(n) spectral library was applied to the assignment of these PA-oligosaccharide isomers in IgG.

Collision-activated infrared multiphoton dissociation in a quadrupole ion trap mass spectrometer.

We propose and demonstrate a new method for multiple-stage mass spectrometry (MSn), collision-activated infrared multiphoton dissociation (CA-IRMPD), which is very effective for the quadrupole ion trap mass spectrometer (QITMS). CA-IRMPD uses a combination of focused laser irradiation (beam radius, approximately 0.4 mm) and collisional activation by a supplemental AC voltage between endcap electrodes.