Provided herein are methods for mapping antibody binding to an immunogen, comprising: immunizing a subject with an immunogen and obtaining sera from the immunized subject at multiple time intervals following immunization, wherein the sera comprises antibodies that are used to form one or more immune complexes with the immunogen; isolating the one or more immune complexes formed by the serum derived antibodies bound to the immunogen; imaging, by electron microscopy, the one or more immune complexes in each of the time intervals, to obtain structural images formed between the immunogen and serum antibodies; determining, from the plurality of structural images, immunogen-antibody binding site for each of the immune complexes obtained at the plurality of time intervals; mapping immunogen-antibody binding by measuring differences in structural images obtained at different time intervals to determine immunogen-antibody binding over multiple time intervals.

Provided are methods and related kits for detection of early stage pancreatic ductal adenocarcinoma. Also provided are methods for treating a patient susceptible, or suspected of being susceptible, to pancreatic ductal adenocarcinoma.

A mass spectrometer is disclosed comprising: an ion detector; ion optics for guiding ions to the ion detector; one or more voltage supply for supplying voltages to said ion optics; control circuitry for controlling the one or more voltage supply so as to switch the ion optics between operating in a first mode in which the ion optics are unable to transmit ions having a first mass to charge ratio or first polarity to the ion detector and a second mode in which the ion optics are able to transmit ions having said first mass to charge ratio or first polarity to the ion detector for a time period; and to repeatedly switch between the first and second modes a plurality of times; and a processor and circuitry configured to: (i) determine the intensity of an ion signal detected by the detector at a first time in each of the time periods that the ion optics are in the second mode; and (ii) determine the intensity of the ion signal detected by the detector at a second, later time in each of the time periods that the ion optics are in the second mode.

A method of calibrating and/or tuning a mass spectrometer includes the steps of: (i) providing a sample; (ii) producing ions from a surface of the sample by means of an ion-producing method, and (iii) using said ions to calibrate a mass spectrometer, tune a mass spectrometer or a combination thereof, wherein the ion producing method is desorption electrospray ionisation (DESI). A vacuum-deposited PLA glass slide can also be used as a calibration/tuning sample for any ion-producing method, e.g. DESI, MALDI or SIMS.

A method for optimizing at least one parameter setting of at least one mass spectrometry device (110) operating at unit resolution is disclosed. The method comprises the following steps: a) determining at least one analyte detection window for detecting an analyte of interest with the mass spectrometry device (110), wherein the analyte detection window is defined by a central mass to charge ratio value of the analyte and a predefined width, wherein the central mass to charge ratio value of the analyte is set to a theoretical mass to charge ratio value of the analyte of interest having more than one decimal place and/or a mass to charge ratio value of the analyte of interest determined by a high resolution mass spectrometry measurement having more than one decimal place; b) determining at least one internal standard detection window for detecting an internal standard substance with the mass spectrometry device (110), wherein the internal standard detection window is defined by a central mass to charge ratio value of the internal standard substance and the pre-defined width, wherein the central mass to charge ratio value of the internal standard substance is set to a mass to charge ratio value of the internal standard substance calculated relative to the analyte of interest and having more than one decimal place and/or to a mass to charge ratio value of the internal standard substance determined by a high resolution mass spectrometry measurement having more than one decimal place.

Embodiments provide methods of disambiguating the spectra produced by cyclic ion analysers. Systems, methods, and computer readable media described herein can compare two sets of ion data that have been obtained using different analyser settings such that the number of passes N through the cyclic segment of the ion path taken by ions contributing to an ion peak can be determined. As a result of the determination of the number of passes N taken by ions, the physicochemical property of those ions can be unambiguously assigned to the ion peak.

A method for detecting radicals in process gases in a semiconductor fabrication assembly is provided where the semiconductor fabrication includes a plasma source and a mass spectrometer with an ion source. The method includes separating ions from the process gases and determining a fixed electron energy in which to measure the process gases. Process gases in the semiconductor fabrication assembly are continuously sampled. A first measurement is performed on the sampled process gases at the electron energy using the mass spectrometer, where the first measurement is performed with the plasma source off. A second measurement of the sampled process gases is performed at the fixed electron energy using the mass spectrometer, where the second measurement is performed with the plasma source on. An amount of a radical present in the sampled process gases is determined as a difference between the second measurement and the first measurement.

An ionizing system includes a flange device for connection to a mass spectrometer or ion mobility spectrometer having the property of providing a barrier between the lower pressure region of the spectrometer and a higher pressure region substantially at atmospheric pressure, and a channel therethrough providing fluid communication between the higher and lower pressure regions. A plate device independent of the flange device which can accommodate multiple samples, such as a sample plate device, when placed over the channel in the flange device substantially seals the channel Sliding the sample plate device while in intimate contact with the flange device provides a means to sequentially and rapidly expose said samples to the opening of the channel and thus the lower pressure region. Samples are ionized when exposed to the lower pressure region in as little as one sample per second using multiple ionization methods.

The invention generally relates to systems and methods for performing multiple precursor, neutral loss and product ion scans in a single ion trap. In certain aspects, the invention provides systems including a mass spectrometer having a single ion trap, and a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply at least one of the following ion scans to a single ion population in the single ion trap: multiple precursor ion scans, a plurality of segmented neutral loss scans, or multiple simultaneous neutral loss scans.

In one aspect, a method for performing mass spectrometry is disclosed, which comprises using a Fourier transform mass analyzer, which extends from an inlet port to an outlet port, to acquire a first mass spectrum of a first plurality of ions generated by ionizing a sample, where the first plurality of ions are radially confined within the mass analyzer under a first radial confinement condition. The method further includes using the Fourier transform mass analyzer to acquire a second mass spectrum of a second plurality of ions generated by ionizing the sample, where the second plurality of ions are radially confined within said mass analyzer using a second radial confinement condition, and comparing said first and second mass spectra to identify spurious mass signals.