The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data, and in particular mass spectrometry data obtained by data-independent acquisition. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. To sequence peptides from mass spectrometry data obtained by data-independent acquisition, precursor profiles representing intensities of one or more precursor ion signals associated with a precursor retention time and fragment ion spectra representing signals from fragment ions and fragment retention times are fed into a neural network.

Systems and methods are described for integrated decomposition and scanning of a semiconducting wafer, where a single chamber is utilized for decomposition and scanning of the wafer of interest.

A method for mass spectral analysis of molecules based on full mass spectral profile or raw scan mode data, comprising the steps of specifying the basic building blocks for the molecule; estimating initial values including trial numbers of building blocks, charge states, and possible modifications; calculating discrete isotope distributions based on elemental compositions; calculating a profile mode theoretical mass spectrum using a target mass spectrum peak shape function; performing regression analysis between acquired profile mode mass spectrum data and calculated theoretical mass spectrum data and reporting regression statistics; using regression statistics as feedbacks to update initially estimated values including trial numbers of building blocks, charge states, and possible modifications; and repeating selected step to optimize the regression statistics. A mass spectrometer operating in accordance with the method. A medium having computer readable program instructions for causing a mass spectrometer associated with a computer to operate in accordance with the method.

A sample support is a sample support for sample ionization, including: a substrate formed with a plurality of through holes opening to a first surface and a second surface on a side opposite to the first surface; a conductive layer provided not to block the through hole in the first surface; and a frame body provided in a peripheral portion of the substrate to surround an ionization region in which a sample is ionized when viewed in a thickness direction of the substrate, in which a marker for recognizing a position in the ionization region is provided in the frame body.

A method for characterizing or quantifying one or more proteins in visible and/or sub-visible particles formed in a sample by detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

An analysis method includes: performing liquid chromatography using a mobile phase including an adsorption prevention agent for preventing adsorption of a sample including a compound having a phosphate group to metal; and performing mass spectrometry on an eluate of the liquid chromatography. The adsorption prevention agent includes an oxalic acid or a salt of the oxalic acid.

The invention relates to a mass spectrometer, a mass spectrometry method and a detection system. The mass spectrometer includes a vacuum chamber having a working pressure being 0.1 Pa≤P≤10 Pa; a linear ion trap, arranged in the vacuum chamber, wherein a field radius r of the linear ion trap is r≤5 mm; and a power supply, configured to provide a radio-frequency voltage for the linear ion trap, a frequency f of the radio-frequency voltage being 2 MHz≤f≤10 MHz. Because a vacuum level is relatively low, this vacuum condition may be realized by selecting a roughing pump for evacuating; and compared with a combined pump unit which is generally selected by a traditional mass spectrometer using the linear ion trap and is composed of a turbo molecular pump and a roughing pump, the roughing pump has a lower pumping speed, smaller size and lower manufacturing cost.

A secondary ion mass spectrometer comprising a primary ion beam device, and means for collecting, mass filtering and subsequently detecting secondary ions released from a sample due to the sample having been impacted by a plurality of primary ion beams. The secondary ion mass spectrometer is remarkable in that it uses a plurality of primary ion beams in parallel for scanning the surface of the sample.

One mode is a method for the structural analysis of an organic compound by MALDI mass spectrometry, including: a sample preparation process (S1) which includes preparing a sample by mixing a specimen containing an organic compound to be analyzed with a predetermined matrix at a mixture ratio within a range from 1:5 to 1:5000 in molar ratio; a mass spectrometry process (S3) which includes irradiating the prepared sample with a laser beam having a spot size equal to or smaller than 15 μm to generate ions originating from a component of the specimen in the sample, and performing a mass spectrometric analysis of the generated ions; and an analyzing process (S4) which includes detecting, from a mass spectrum acquired in the mass spectrometry process, ions including product ions resulting from in-source decay, and estimating the structure of the organic compound to be analyzed based on information concerning the ions.

A measurement section (1) performs a mass spectrometric analysis for each micro area within a measurement area on a sample. A dimension reduction processor (23) performs data processing by non-linear dimension reduction using manifold learning on mass spectrometric data for each micro area, to obtain, for each micro area, a set of data reduced to three dimensions from the dimensions corresponding to the number of mass-to-charge-ratio values. A display color determiner (24) determines a color for each of the points corresponding to the data of the micro areas after the dimension reduction, by arranging those points within a three-dimensional space having three axes representing the three dimensions, with three primary colors respectively assigned to the three axes. A segmentation image creator (25) creates a segmentation image corresponding to the measurement area or a partial area in the measurement area, by arranging, on two dimensions, pixels which respectively correspond to the points within the three-dimensional space, where each pixel has a color given to the point corresponding to the pixel and is located according to the position within the measurement area of the micro area corresponding to the point.