Method for producing multiply-charged helium nanodroplets and charged dopant clusters and nanoparticles out of the helium nanodroplets, the method comprising: producing neutral helium nanodroplets in a cold head (1) via expansion of a pressurized, pre-cooled, supersonic helium beam of high purity through a nozzle (3) into high vacuum with a base pressure under operation preferably below 20 mPa, ionizing the helium nanodroplets by electron impact (15), wherein the electron impact (15) leads to multiply-charged helium nanodroplets, doping the charged helium nanodroplets with dopant vapor in the pickup cell (19), wherein the doped nanodroplets form cluster ions with the initial charges acting as seeds, wherein the size of the nanoparticles can vary from a few atoms up to 105 atoms by arranging the size of the neutral helium nanodroplets, the charge of the helium nanodroplets and the density of dopant vapor in the pickup cell (19).

A method and apparatus for conducting reactions between precursor ions and reagent ions, for example, a reaction between a precursor cation and an electron, such as ECD, are disclosed. The apparatus comprises first, second, and third pathways, each of which extends at least partially along a central axis, and wherein the second central axis is orthogonal to the first and third central axes. Charged species can be introduced into the second pathway as the ions are transmitted therethrough, thereby increasing precursor ion and charged species interaction without simultaneous trapping of the species.

A method and apparatus for analyzing samples using mass spectrometry are disclosed. The apparatus includes a reaction device configured to dissociate sample ions into fragments by reacting the sample ions with a charged species (e.g., electrons) such as through ECD, EID, or EIEIO. The kinetic energy of the charged species is such that the fragments may be detected and produce spectra that allow for the determination of isomeric species in the sample and the location of double bonds of sample molecules. The fragments may include radical fragments and non-radical fragments. The apparatus may also include an oxygen gas source configured to react with the radical fragments to produce oxygen-radical fragments. Spectra resulting from analysis of the fragments may allow for the determination of the oxygen-radical fragments resulting from the dissociation of the sample molecules.

A method and apparatus for conducting ion to charged species reactions, more particularly reactions wherein the charged species is an electron, such as ECD. The apparatus comprises first and second pathways which are orthogonal to one another. The first pathway through which ions are introduced comprises multiple multipoles with a gap situated there between. The second pathway introduces the charged species through the gap orthogonally to the first pathway. In this way, a cross-type reaction device allows ion-charged species interactions to occur.

A linear ion trap includes at least two discrete trapping regions for processing ions and at least one gas pulse valve for applying pulses of gas to dynamically control pressure in the at least two discrete trapping regions. A RF electrical potential generator produces two RF waveforms, each applied to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially. A multi-output DC electrical potential generator produces multiple DC field components superimposed to the RF trapping field component and distributed across the length of the linear ion trap to control ions axially. A control unit is configured to switch the DC electrical potentials and corresponding DC field components collectively forming a first trapping region of the at least two discrete trapping regions that is populated with ions to alter ion potential energy from a first level to a second level, and to enable at least a first ion processing step in at least one of the first and second levels.

A linear ion trap includes at least two discrete trapping regions for processing ions, a RF electrical potential generator, a multi-output DC electrical potential generator, and a control unit. The RF electrical potential generator produces two RF waveforms each applied to a pair of pole electrodes of the linear ion trap forming a RF trapping field component to trap ions radially. The multi-output DC electrical potential generator produces multiple DC field components superimposed to the RF field component and distributed across the length of the linear ion trap to control ions axially. The control unit switches the DC electrical potentials and corresponding DC field components collectively forming a first trapping region populated with ions to alter ion potential energy from a first level to a second level, and enables a first ion processing step in at least one of the first and second levels.

Systems and methods described herein can provide for top down mass spectrometric analysis of proteins or peptides in a sample using ExD, in some aspects via direct infusion of the sample to the ion source without on-line LC separation, while deconvoluting the ambiguity in the ExD spectra generated by impure samples. For example, methods and systems in accordance with various aspects of the present teachings can utilize patterns in charge-reduced species following ExD to correlate the ExD fragments with their precursor ions in order to more confidently identify the precursor ion from which the detected product ions originated.

A method of mass spectrometry is disclosed comprising: providing supercharged analyte ions; and supplying electrons or reagent ions to said analyte ions so as to transfer charge from said reagent ions or electrons to said analyte ions, said transfer of charge causing at least some of said analyte ions to dissociate. The charge transfer step is performed at a relatively high pressure and preferably substantially at atmospheric pressure.

Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

Methods and system that determines disulfide and trisulfide linkages within analytes (e.g., polypeptides) is described. In certain aspects. a sample comprising polypeptides (such as an antibody) may be subjected to dissociation using an electron activated dissociation (which can include electron capture dissociation and electron transfer dissociation) and the fragmentated portions are analyzed using a mass spectrometer to produce a spectrum. The spectrum is analyzed by a processor to identify peaks from the spectrum that are related to one another in the spectra by a separation of 32 mass units. In identifying an antibody comprising peptide segments linked via a trisulfide bond. for example, four different peaks representing two different peptides are searched for and identified representing a first peptide portion having mass/charge of A and A+32 and a second peptide having mass/charge of B and B+32.