Abstract: The present disclosure provides a “looping amplification” method to increase the specificity of nucleic acid amplification. This increased specificity facilitates multiplexing to a much higher degree than was previously possible.

Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.

Abstract: Methods and systems for automated slide handling for imaging applications are described herein. In certain aspects, an automated slide handler may be operatively coupled to a slide hotel and/or one or more imaging systems described herein. The automated slide handler may be a robotic arm with up to 6 degrees of freedom. Automated slide handling may include sample preparation, such as sectioning and staining. Suitable imaging systems include a fluorescence microscope or an imaging mass cytometer. Methods and systems disclosed herein enable high throughput profiling of tissue sections.

Abstract: A microscopy apparatus comprises a microscope comprising a stage configured to hold a tissue sample, a UV laser assembly configured to emit a UV laser beam to a viewing area of the tissue sample, and an IR laser assembly configured to emit an IR laser beam to the viewing area of the tissue sample. The UV and IR laser assemblies are oriented so as to emit the respective UV and IR laser beams in a same direction.

Abstract: Embodiments of the present invention relate to replacement of the previous ICP-based ionisation system with a new laser ionisation system, providing improved mass spectrometer-based apparatus and methods for using them to analyse samples, in particular the use of mass spectrometry mass cytometry, imaging mass spectrometry and imaging mass cytometry, for the analysis of biological samples. Accordingly, embodiments of the present invention provide an apparatus, for example a mass cytometer, comprising: 1) a sampler; 2) a laser ionisation system to receive material removed from the sample by the sampler, wherein the laser ionisation system comprises an ionisation system conduit and a pulsed laser adapted to ionise sample material passing through or exiting the ionisation system conduit; and 3) a mass spectrometer to receive elemental ions from said ionisation system and to analyse said elemental ions.

Abstract: A new class of mass-tag polymers is provided, which include enriched metal isotopes such as zirconium and hafnium mass tags. The chemistry of these new mass tags are different from that of lanthanide mass tags, and opens up new mass channels that can be used in mass cytometry. These polymers may be used for mass cytometry, therapeutic delivery of a radioactive isotope, or screening of a therapeutic isotope. Aspects include a kit, method of making, and method of using a polymer, isotopic composition, or both. A kit may include a polymer. The polymer may include pendant groups that chelate an enriched isotope, such as zirconium and/or hafnium. The kit may include an isotopic composition comprising an enriched zirconium or hafnium isotope. Polymers may be conjugated to a biologically active material. Aspects may also include making a kit. Aspects include use of a kit, such as for mass cytometry.

Abstract: The present invention relates to the high resolution imaging of samples using imaging mass spectrometry (IMS) and to the imaging of biological samples by imaging mass cytometry (IMC™) in which labelling atoms are detected by IMS. LA-ICP-MS (a form of IMS in which the sample is ablated by a laser, the ablated material is then ionised in an inductively coupled plasma before the ions are detected by mass spectrometry) has been used for analysis of various substances, such as mineral analysis of geological samples, analysis of archaeological samples, and imaging of biological substances. However, traditional LA-ICP-MS systems and methods may not provide high resolution. Described herein are methods and systems for high resolution IMS and IMC.

Abstract: A lyophilized antibody panel is disclosed for interrogation using elemental analysis. The antibody panel includes multiple antibodies each element-tagged or element-labelled with one or more isotopes such that each different antibody is isotopically distinguishable from the other antibodies. Each element tag can include one or more unique isotopes or unique combinations of isotopes. The set of element-tagged antibodies can be lyophilized in admixture. Thus, the lyophilized element-tagged antibody panel can be easily and efficiently resuspended and mixed with a sample prior to interrogation with an elemental analyzer, such as a mass spectrometer. This lyophilized element-tagged antibody panel can provide the benefits of an element-tagged assay while also being easy to use and remaining stable for long durations.

Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.

Abstract: Inductively coupled plasma (ICP) analyzers use an ICP torch to generate a plasma in which a sample is atomized an ionized. Analysis of the atomic ions can be performed by atomic analysis, such as mass spectrometry (MS) or atomic emission spectrometry (AES). Particle based ICP analysis includes analysis of particles such as cells, beads, or laser ablation plumes, by atomizing and ionizing particles in an ICP torch followed by atomic analysis. In mass cytometry, mass tags of particles are analyzed by mass spectrometry, such as by ICP-MS. Systems and methods of the subject application include one or more of: a demountable ICP torch holder assembly, an external ignition device; an ICP load coil comprising an annular fin, particle suspension sample introduction fluidics, and ICP analyzers thereof.

Abstract: The present disclosure provides a “looping amplification” method to increase the specificity of nucleic acid amplification. This increased specificity facilitates multiplexing to a much higher degree than was previously possible.

Abstract: The present invention relates to the high resolution imaging of samples using imaging mass spectrometry (IMS) and to the imaging of biological samples by imaging mass cytometry (IMCTM) in which labelling atoms are detected by IMS. LA-ICP-MS (a form of IMS in which the sample is ablated by a laser, the ablated material is then ionised in an inductively coupled plasma before the ions are detected by mass spectrometry) has been used for analysis of various substances, such as mineral analysis of geological samples, analysis of archaeological samples, and imaging of biological substances. However, traditional LA-ICP-MS systems and methods may not provide high resolution. Described herein are methods and systems for high resolution IMS and IMC.

Abstract: Described herein are methods, kits and systems for sample enrichment, multi-step library preparation, sample normalization, detection of sample biomolecules and combinations thereof. Enrichment and multi-step library preparation is described in the context of microfluidic workflows. Sample barcoding methods and kits are described for increasing sample throughput while reducing background in negative samples. Integrated microfluidic devices comprising sample processing unit cells coupled to an array of reaction sites are provided for integrated workflows.

Abstract: We describe in this application the analysis of samples using elemental or mass spectrometry and the analysis of samples, such as biological samples by suspension mass cytometry or imaging mass cytometry and an inductively coupled plasma torch with reverse vortex flow for elemental analysis and a method of operating an ICP torch configured to interface with a spectrometer.

Abstract: As described herein, one or more parameters of a direct ionization imaging mass spectrometer (IMS) may be set to obtain a desired plasma and deliver it to a mass detector. Depending on the application, certain parameters may be predetermined (e.g., a spot size given a desired resolution) and, as described herein, other parameters can be adjusted to obtain the desired plasma properties. Also included is sample preparation suitable for direct ionization IMS and/or other imaging modalities.

Abstract: We describe in this application systems and methods for autofocusing in imaging mass spectrometry. The present application describes improvements over current IMS and IMC apparatus and methods through an autofocus component including a plurality of apertures in the autofocus system, such as a plurality of apertures arranged in 2 dimensions. As a plurality of apertures is used, the autofocus system provides redundancy in the event that measurement of focus on the sample from the illuminating radiation passed through one or more of the apertures fails so as to reduce the number of unsuccessful autofocus attempts.

Abstract: This disclosure relates to reagents and their use for elemental imaging mass spectrometry of biological samples.

Abstract: This disclosure relates to systems and methods for high speed modulation sample imaging. Disclosed herein are systems and methods for performing imaging mass cytometry, including analysis of labelling atoms by elemental (e.g., atomic) mass spectrometry. Aspects include a sampling system having, and method of using, a femtosecond (fs) laser and/or laser scanning. Alternatively or in addition, aspects include systems and methods for co-registering other imaging modalities with imaging mass cytometry.

Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.

Abstract: The present disclosure provides a “looping amplification” method to increase the specificity of nucleic acid amplification. This increased specificity facilitates multiplexing to a much higher degree than was previously possible.