A system and method to screen a plurality of molecules in datasets obtained from mass spectroscopy, including selecting and receiving at least one dataset of mass spectral data, and selecting customizable m/z mass tolerance peaks to assign initial compound assignments from at least one adduct ion hierarchy database for at least one compound having a parent molecule. Adduct ion hierarchy screening is applied to at least a portion of the dataset, wherein selected dataset features are tested to determine if they represent the most abundant expected adduct of the parent molecule class and if the expected adduct assignment hierarchy are present in the dataset.

The invention is related to a trapped ion mobility spectrometer (TIMS device) and proposes to use higher order (order N>2) linear multipole RF systems to accumulate and analyze ions at an electric DC field barrier, either pure higher order RF multipole systems or multipole RF systems with transitions from higher order towards lower order, e.g. from a linear octopolar RF system (N=4) to a linear quadrupole RF system (N=2) in front of the apex of the electric DC field barrier.

A plasma generating device includes: a chamber which is equipped with a dielectric wall structure and into which sample gas to be measured flows; an RF supplying mechanism that generates plasma inside the chamber using an electric field and/or a magnetic field through the dielectric wall structure; and a floating potential supplying mechanism that includes a first electrode disposed along an inner surface of the chamber. The RF supplying mechanism may include an RF field forming unit disposed in a first direction with respect to the chamber and the first electrode may include an electrode disposed in a second direction with respect to the chamber.

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (LCMS). Detection in a high-resolution, accurate mass (HRAM) MS1 spectrum of a precursor ion matching an isotopically-labeled peptide triggers acquisition of an MS/MS spectrum (preferably acquired in an ion trap or other fast mass analyzer) to determine if a product ion is present matching a characteristic product ion (e.g., the y.sub.1 ion) of the isotopically-labeled peptide. If the characteristic product ion is present, then a HRAM MS/MS spectrum is acquired for detection and quantitation of the corresponding endogenous peptide.

A mass analyzer includes a main substrate, an upper substrate adhered to the main substrate, and a lower substrate. A mass analysis room (cavity) is formed in the main substrate and penetrates from an upper surface of the first main substrate to a lower surface of the first main substrate. A vertical direction (Z direction) to the main substrate by the upper substrate, both sides of the lower substrate, a travelling direction (X direction) of charged particles and a right angle to the Z direction by the main substrate, and both sides of a right-angled direction (Y to Z direction) and the X direction by a side surface of the main substrate are surrounded. A central hole is open in the side plate of the main substrate that the charged particles enter. The charged particles enter the mass analysis room through the central hole formed in the first main substrate.

A mass spectrometer includes an ion source, an ion guide, a quadrupole mass filter, a detector, DC and RF power sources, and a voltage control device for controlling an acceleration voltage by controlling the power source. The voltage controller controls the acceleration voltage such that it is increased as the mass-to-charge ratio of ions to be measured is increased within a control region. The control region is surrounded, having one coordinate axis representing the mass-to-charge ratio of the ions passing the ion guide and another axis representing the acceleration voltage applied to the ion guide, by a line representing a lower limit of a stable region where the ions pass the ion guide stably, a line representing an ion mobility of the ions, an upper side representing an upper limit of the acceleration voltage, and a lower side representing a value at which the acceleration voltage is zero.

An ion analyzer including: a base member fixed to a ion outflow port and having a cylindrical concave part; a cylindrical first conductive member accommodated in the concave part; a first ion flow controller fixed to an exposed end of the first conductive member; a cylindrical insulating member inserted into the first conductive member; a rod-shaped second conductive member inserted into the insulating member; a second ion flow controller being fixed to an exposed end of the second conductive member; a first power feeding unit that, when accommodated in the concave part, comes into contact with the first conductive member; and a second power feeding unit that, when accommodated in the concave part, comes into contact with the second conductive member when the first conductive member accommodates the second conductive member and the insulating member.

In DM-SWATH a plurality of CoVs and a precursor ion mass range are received. A processor performs an iterative series of steps for each CoV of the plurality of CoVs. For each CoV of the plurality of CoVs, the CoV is applied to the DMS device to select a group of precursor ions. A mass filter is instructed to select precursor ions of the group that are within the precursor ion mass range, producing a subgroup of precursor ions. A fragmentation device is instructed to fragment the subgroup of precursor ions, producing a group of product ions. A mass analyzer is instructed to measure the intensity and m/z of the group of product ions, producing a product ion spectrum for each CoV of the plurality of CoVs. DM-SWATH is further used to validate if a known compound is in a sample.

Measurement of a standard sample is repeated under control of an analysis control unit (94) while a CD voltage applied to a conversion dynode (61) of a detection unit (6) is gradually changed by a CD voltage adjustment unit (96). Then, every time a measured mass spectrum is obtained, a spectrum pattern determination unit (93) determines whether a pattern of the measured mass spectrum matches a pattern of a standard mass spectrum of a standard sample in a compound database (92), and determines the CD voltage at the time of being regarded as matching to be the set value. When the pattern of the mass spectrum is adjusted by changing the voltage applied to the ion lens (3), performance such as sensitivity is likely to be unstable due to stain on the lens electrode or the like, but since the detection unit (6) is unlikely to be affected by such a stain, unstable performance can be avoided.

Disclosed herein is an ion guide for guiding an ion beam along an ion path, said ion guide having a longitudinal axis which corresponds to said ion path. Said ion guide comprises a plurality of electrode plates which are arranged perpendicularly to the longitudinal axis, each electrode plate having an opening and being arranged such that said longitudinal axis extends through its respective opening, wherein said openings collectively define an ion guide volume. The ion guide extends or is configured to extend through a separation wall separating adjacent first and second pumping chambers. The ion guide has a first portion, in which gaps are formed between at least some of said electrode plates such that uncharged gas can escape from said ion guide volume, wherein said first portion is completely located in said first pumping chamber. A second portion, in which sealing elements are arranged between adjacent electrode plates, prevents neutral gas from escaping from that portion of the ion guide volume between adjacent electrode plates, said second portion extends at least from said separation wall into said second pumping chamber.