A dissociation device fragments a precursor ion, producing at least two different product ions with overlapping m/z values in the dissociation device. The dissociation device applies an AC voltage and a DC voltage creating a pseudopotential that traps ions below a threshold m/z including the at least two product ions. The dissociation device receives a charge reducing reagent that causes the trapped at least two product ions to be charge reduced until their m/z values increase above the threshold m/z set by the AC voltage. The increase in the m/z values of the at least two product ions decreases their overlap. The at least two product ions with increased m/z values are transmitted to another device for subsequent mass analysis by applying the DC voltage to the dissociation device relative to a DC voltage applied to the other device.

A method of analyzing molecules, comprising: generating ions from a sample of molecules; cooling the generated ions below ambient temperature; fragmenting at least some of the cooled ions by irradiating the ions with light at a plurality of different wavelengths (λ) within one or more predetermined spectral intervals; recording a fragment mass spectrum of the fragmented ions comprising a detected signal (I) versus m/z over a predetermined range of m/z values for each of the plurality of different wavelengths (λ), thereby recording a two-dimensional dependency of the detected signal (I) on m/z and irradiation wavelength (λ); and determining from the recorded two-dimensional dependency an identity of at least one of the generated ions and/or relative abundances of different generated ions and thereby determining an identity of at least of one of the molecules and/or relative abundances of different molecules in the sample.

An ion-mobility spectrometer system includes a housing with an upstream end, a downstream end, and a drift region defined along a longitudinal axis through the housing between the upstream and downstream ends. A first ionizer is operatively connected the housing to supply ions at the upstream end. A second ionizer is operatively connected to the housing to supply ions at the upstream end, wherein the first and second ionizers are both situated upstream of the drift zone relative to an ion flow path through the drift zone. An electric field generator is operatively connected to the housing to drive ions through the drift zone in a direction from the upstream end toward the downstream end. The second ionizer is a radioactive ionizer mounted to the housing at the upstream end positioned to direct irradiated ions into the housing.

The present invention concerns a method for sequencing oligosaccharides, which makes it possible to identify the primary sequence of an oligosaccharide of unknown structure, including its monosaccharide composition, the position (regiochemistry) and configuration (stereochemistry) of glycosidic bonds, the nature and position of functional modifications, and its branched structure, particularly including the identification of the reducing end.

The invention proposes a methods and devices for tandem ion mobility spectrometry using at least one TIMS analyzers (TIMS=trapping ion mobility spectrometry), in particular in the field of structural biology.

Methods are described for using a combination of mass spectroscopic and proteomic approaches for identifying the specific pairing of heavy and light chains for an intact antibody, an antibody fragment, a mixture of intact antibodies, or a mixture of antibody fragments.

A method of analyzing molecules, comprising: generating ions from a sample of molecules; cooling the generated ions below ambient temperature; fragmenting at least some of the cooled ions by irradiating the ions with light at a plurality of different wavelengths () within one or more predetermined spectral intervals; recording a fragment mass spectrum of the fragmented ions comprising a detected signal (I) versus m/z over a predetermined range of m/z values for each of the plurality of different wavelengths (), thereby recording a two-dimensional dependency of the detected signal (I) on m/z and irradiation wavelength (); and determining from the recorded two-dimensional dependency an identity of at least one of the generated ions and/or relative abundances of different generated ions and thereby determining an identity of at least of one of the molecules and/or relative abundances of different molecules in the sample.

The present invention provides a method for specifically cleaving a C-C bond of a peptide backbone and/or a side chain of a protein and a peptide, and a method for determining amino acid sequences of protein and peptide. A method for specifically cleaving a C-C bond of a peptide backbone and/or a side chain bond of a protein or a peptide, comprising irradiating a protein or a peptide with laser light in the presence of at least one hydroxynitrobenzoic acid selected from the group consisting of 3-hydroxy-2-nitrobenzoic acid, 4-hydroxy-3-nitrobenzoic acid, 5-hydroxy-2-nitrobenzoic acid, 3-hydroxy-5-nitrobenzoic acid, and 4-hydroxy-2-nitrobenzoic acid. A method for determining an amino acid sequence of a protein or a peptide, comprising irradiating a protein or a peptide with laser light in the presence of the above specific hydroxynitrobenzoic acid to specifically cleave a C-C bond of a peptide backbone and/or a side chain bond, and analyzing generated fragment ions by mass spectrometry.

A method of analyzing molecules, comprising: generating ions from a sample of molecules; cooling the generated ions below ambient temperature; fragmenting at least some of the cooled ions by irradiating the ions with light at a plurality of different wavelengths () within one or more predetermined spectral intervals; recording a fragment mass spectrum of the fragmented ions comprising a detected signal (I) versus m/z over a predetermined range of m/z values for each of the plurality of different wavelengths (), thereby recording a two-dimensional dependency of the detected signal (I) on m/z and irradiation wavelength (); and determining from the recorded two-dimensional dependency an identity of at least one of the generated ions and/or relative abundances of different generated ions and thereby determining an identity of at least of one of the molecules and/or relative abundances of different molecules in the sample.

An electrostatic ion trap or an array of electrostatic ion traps are provided having a longitudinal length of no more than 10 mm and/or at least one electrode with a capacitance to ground of no more than 1 pF. First and second sets of planar electrodes may be distributed along the longitudinal axis, at least some of the which are configured to receive an electrostatic potential for confinement of ions received in the space between the first and second sets of planar electrodes. An array may comprise an inlet for receiving an ion beam, configured such that a portion of the ion beam can be trapped in each of the ion traps. Signals indicative of ion mass and charge data may be obtained from multiple electrostatic ion traps in the array. This mass and charge data may be combined for identification of components of a mixture of different analyte ions.