A method for performing library-free search analysis including performing a search using a spectrum-centric approach for a data; performing at least one of improving peptide centric analysis of a predicted spectral library by using the results of the spectrum centric search for creating a sub-selection of precursors, including a calibration by using results from the spectrum-centric approach; creating an optimized predicted library by refining static prediction models; using the calibration and/or the optimized predicted library to initiate a peptide-centric search for the data based on an in-silico library; creating a curated library by combining the results of the spectrum-centric approach with the results from the peptide-centric approach; and analyzing the results of the curated library using a second peptide-centric search of the data.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Recorded and downloadable software application for the
setup, tasks orchestration, and parallelized execution of
mass spectrometry data analysis (including but not limited
to proteomics and metabolomics); recorded and downloadable
software application for setting up, distributing, and
parallelizing computational tasks in the field of mass
spectrometry, on cloud and high-performance computing (HPC)
environments; recorded and downloadable software
applications for submitting, tracking, and monitoring
computational tasks related to mass spectrometry data
analysis; recorded and downloadable software application for
centralizing processing of mass spectrometry (MS) data for a
given institution, allowing user administration and
management for job submission, tracking and prioritization;
recorded and downloadable software applications for
processing large-scale scientific datasets (big MS data),
including mass spectrometry-based (MS-based) proteomics and
metabolomics data; recorded and downloadable software
application for reporting, managing and storing results of
MS data processed in cloud or high-performance computing
(HPC) environments; recorded and downloadable software for
capturing, storing, and organizing metadata related to mass
spectrometry data processing; recorded and downloadable
software application for monitoring workflow status and task
progress; software tools for workflow automation and job
scheduling, in computational biology and bioinformatics. Software as a service (SaaS) for the configuration,
distribution and scaling of scientific data analysis
workflows in the fields of mass spectrometry and omics
research; Cloud-based services for processing and
visualizing mass spectrometry and omics data using computing
technologies; technical support and information services in
connection with software tools for omics data analysis;
development and hosting of software platforms enabling
workflow monitoring, job tracking, and metadata management.
09 - Scientific and electric apparatus and instruments
Goods & Services
Recorded and downloadable computer software platforms for
analyzing data-independent acquisition (DIA)
mass-spectrometry data of omics and multi-omics experiments,
including proteomics, peptidomics and/or metabolomics;
recorded and downloadable software for the quantitative
profiling of proteins, peptides and/or metabolites in
various biological samples; recorded and downloadable
software for analyzing liquid chromatography-mass
spectrometry (LC-MS) data, including data acquired with ion
mobility dimension; recorded and downloadable software for
empirical search space generation, data identification, and
extraction of quantitative values from data-independent
acquisition (DIA) data, across multiple omics approaches;
recorded and downloadable software for post-analysis data
inspection, visualization, validation and customizable
reporting; recorded and downloadable software employing
artificial intelligence (AI) and machine learning for
peptide and/or metabolite identification, quantification and
multi-omic data analysis; recorded and downloadable software
for generating and utilizing data-dependent acquisition
(DDA), data-independent acquisition (DIA) and hybrid
libraries across multiple proteomics, peptidomics and
metabolomics projects; recorded and downloadable software
for differential abundance analysis, sample clustering and
annotating for DIA acquired LC-MS proteomics, peptidomics
and metabolomics data.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Recorded and downloadable software application for the setup, tasks orchestration, and parallelized execution of mass spectrometry data analysis, including but not limited to, proteomics and metabolomics; recorded and downloadable software application for setting up, distributing, and parallelizing computational tasks in the field of mass spectrometry, on cloud and high-performance computing (HPC) environments; recorded and downloadable software applications for submitting, tracking, and monitoring computational tasks related to mass spectrometry data analysis; recorded and downloadable software application for centralizing processing of mass spectrometry (MS) data for a given institution, allowing user administration and management for job submission, tracking and prioritization; recorded and downloadable software applications for processing large-scale scientific datasets being big MS data, including mass spectrometry-based (MS-based) proteomics and metabolomics data; recorded and downloadable software application for reporting, managing and storing results of MS data processed in cloud or high-performance computing (HPC) environments; recorded and downloadable software for capturing, storing, and organizing metadata related to mass spectrometry data processing; recorded and downloadable software application for monitoring workflow status and task progress; software tools being recorded and downloadable computer software for workflow automation and job scheduling, in computational biology and bioinformatics Software as a service (SaaS) featuring software for the configuration, distribution and scaling of scientific data analysis workflows in the fields of mass spectrometry and omics research; Cloudbased services, namely, providing temporary use of non-downloadable cloud-based software for processing and visualizing mass spectrometry and omics data using computing technologies; technical support in the nature of troubleshooting of computer software problems using provided SaaS solution and information services in connection with software tools for omics data analysis; development and hosting of software platforms enabling workflow monitoring, job tracking, and metadata management
09 - Scientific and electric apparatus and instruments
Goods & Services
Recorded and downloadable computer software platforms for analyzing data-independent acquisition (DIA) mass-spectrometry data of omics and multi-omics experiments, including proteomics, peptidomics and/or metabolomics; recorded and downloadable software for the quantitative profiling of proteins, peptides and/or metabolites in various biological samples; recorded and downloadable software for analyzing liquid chromatography-mass spectrometry (LC-MS) data, including data acquired with ion mobility dimension; recorded and downloadable software for empirical search space generation, data identification, and extraction of quantitative values from data-independent acquisition (DIA) data, across multiple omics approaches; recorded and downloadable software for post-analysis data inspection, visualization, validation and customizable reporting; recorded and downloadable software employing artificial intelligence (AI) and machine learning for peptide and/or metabolite identification, quantification and multi-omic data analysis; recorded and downloadable software for generating and utilizing data-dependent acquisition (DDA), data-independent acquisition (DIA) and hybrid libraries across multiple proteomics, peptidomics and metabolomics projects; recorded and downloadable software for differential abundance analysis, sample clustering and annotating for DIA acquired LC-MS proteomics, peptidomics and metabolomics data.
6.
SYSTEM AND METHOD FOR TARGETED ANALYSIS OF DIAGONAL FAMILY OF DIA-PASEF ACQUISITION METHODS
The present invention determines how to extract data for a peptide precursor and its fragments in an efficient manner when processing the so-called diagonal family of dia- PASEF acquisition methods, such as synchro-PASEF or midia-PASEF. In one implementation of the invention, the entire ion cloud is treated as if it were acquired by a single diagonal DIA window.
Method for the detection of a conformational state of a protein being in a complex mixture of further proteins and other biomolecules, wherein the protein has been subjected to a condition inducing a structural change, including: limited proteolysis of the extract mixture under a condition in which the protein is in the original conformational state to be detected leading to a first fragment sample; directly followed by (2) removal of large peptides and proteins or other biomolecules from said first fragment sample to form an enriched fragment sample; (3) analytical analysis of the enriched fragment sample for the determination of fragments characteristic of having been the result of the limited proteolysis of (1) as well as remaining after the removal (2) for the determination of the conformational state of said at least one protein.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
38 - Telecommunications services
41 - Education, entertainment, sporting and cultural services
42 - Scientific, technological and industrial services, research and design
Goods & Services
Downloadable computer software using artificial intelligence
in the field of proteomics research; downloadable artificial
intelligence and machine learning software for controlling,
tracking, recording and interpreting data relating to
proteomics; downloadable bioinformatics workflow management
software in the field of proteomics; downloadable software
for tracing out biological diagrams in the field of
proteomics; downloadable software applications for any mass
spectrometry proteomics application; downloadable computer
software intended for collecting, mining, searching,
extracting, managing, analyzing, distributing, sharing and
viewing data; downloadable software for accessing
computerized data used in the field of proteomics;
downloadable software for the collaboration and reporting of
computerized data as well as the viewing of graphical
information, used in the field of proteomics; downloadable
software for viewing data; downloadable software for data
mining in the field of proteomics; downloadable diagnostic
software intended for use in scientific analysis of proteins
not for medical use; downloadable software for analyzing
proteins, proteomes and biological data; downloadable
software for accessing and using databases and information
for research and development services in the fields of
medicine, proteomics and biotechnology; downloadable
software for the automated mining of proteomic data;
downloadable interactive database software; downloadable
database management software in the field of proteomics;
downloadable software for scientific data analysis; recorded
or downloadable data sets in the field of proteomics;
downloadable software being scientific devices; downloadable
data management software for the study of proteins and
peptides in the development of medicines and
pharmaceuticals; downloadable computer databases in the
field of proteomics; downloadable interactive databases in
the field of proteomics; intelligent gateways for data
analysis; downloadable software platforms in the field of
proteomics; downloadable software applications platform
using artificial intelligence for preserving and viewing
data in the field of proteomics; downloadable information
processing systems using artificial intelligence for
proteomic analysis; downloadable software platforms, network
communication devices, mobile applications enabling users to
analyze and mining proteomic data; downloadable electronic
publications in the nature of journals, scientific posters
and research papers in the field of proteomics; downloadable
publications transmitted by electronic means, namely,
reports, directories and reference materials concerning
science. Data processing and management services in the fields of
science and medicine; managing and compiling computer
databases in the field of proteomics; automatic processing
of scientific and medical data; collecting and processing
proteomic data; advice on the management of proteomic data;
compiling and providing statistical information concerning
science; compilation of statistical data for use in
scientific research. Providing an online forum enabling users to share data,
share ideas, consult analytical ideas, mine data and request
support in the field of proteomics; transmitting and
distributing data on computer networks or via the Internet;
providing access and renting out access to computer
databases and to computer networks; providing access to
data, websites, platforms and portals via the Internet;
consulting services relating to data communication. Online publication of specialized journals containing
information connected with the use of software in the fields
of scientific data management and analysis; non-downloadable
electronic publication services in the nature of
newsletters, specialized journals and articles, available
via a website, in the field of protein data management and
protein data analysis; training and online training services
in connection with the use and operation of computer
software programs in the field of protein data management
and protein data analysis; education services provided via
computer databases in the field of proteomics. Providing medical and scientific research information in the
field of pharmaceuticals and clinical trials based on
protein analysis; research services in the field of
proteins, antibodies, micro-organisms and cells using
proteomics technology; product development advice for
inventors in the field of cellular biology using proteomics;
technical research and consulting in the pharmaceutical,
medical, biological and clinical fields using proteomics
technology; providing medical and scientific research
information in the pharmaceutical, medical, biological and
clinical fields using proteomics technology; medical and
scientific research using bioinformatics, namely,
proteomics, proteome studies, proteome design, analysis and
identification of peptides and proteins, and mass
spectrometry; development of pharmaceuticals using
proteomics; scientific research and analysis in the field of
proteomics conducted using databases; technical data
analysis services in the field of proteomics; providing
information on clinical studies in the field of proteomics
via an interactive website; computer-aided scientific and
industrial analysis services in the field of proteomics;
research into the detection of proteins and peptides;
services connected with data science (biostatistics);
pharmaceutical product discovery and development services;
interpreting biological study data; providing a website
obtaining articles, data sheets, infographics, in the field
of proteomics; preparation of reports with respect to
biotechnology; computer services, namely, providing
temporary use of online non-downloadable software for
consulting and analyzing scientific information on proteins
in the fields of pharmaceutical, biological and clinical
sciences; research, design, development, maintenance and
support of computer software for scientific data; design
services concerning scientific data processing tools;
designing and developing artificial intelligence and machine
learning software; software as a service (SaaS) offering
software for access for retrieving, managing, analyzing,
sharing, collaborating, and reporting computerized data as
well as viewing graphic information, used in the fields of
protein data management and protein data analysis; providing
computer software for the collection and analysis of data
for the purpose of protein data mining; providing online
non-downloadable software for database management; temporary
provision of online non-downloadable software for importing
and managing data; providing temporary use of
non-downloadable software for analyzing proteins, proteomes,
and biological data; providing temporary use of
non-downloadable software for graphical representation of
proteomeS and inended for use in the development of
pharmaceuticals; providing temporary use of non-downloadable
software for accessing and using databases and information
intended for research and development services in the fields
of proteomics and biotechnology; providing online
non-downloadable software for enabling scientists and
clinicians to interactively manage and share proteomic data;
providing temporary use of non-downloadable software for
analyzing scientific data and generating reports; biobank
services, namely, electronic data storage and analysis of
biological, clinical, chemical, forensic and
biopharmaceutical substances and samples in a database for
scientific purposes; providing online non-downloadable
information processing systems using artificial intelligence
for proteomic analysis; software as a service with
intelligent gateways in the nature of non-downloadable
software for data analysis in the field of proteomics;
proteomic life sciences computer platform as a service
[PaaS]; development of computer platforms; software as a
service [SaaS] offering software using artificial
intelligence for preserving and viewing data in the field of
proteomics; Platform as a service (PaaS) offering computer
software platforms for accessing, extracting, managing,
analyzing, sharing, collaborating, and reporting
computerized data and viewing graphic information, for use
in the field of proteomics; providing online
non-downloadable software and data platform enabling users
to access data and services related to proteomics; providing
online non-downloadable software platforms for providing
data reports and appraisals in the field of proteomics;
computer platform as a service (PaaS) offering software
platforms for the operation of proteomic data for the
discovery and development of new drugs; electronic storage
of data in a data warehouse; data mining; analyzing
proteomic data; advice on the analysis of proteomic data.
9.
SYSTEM AND METHOD FOR IMPROVING HIGH-PRECISION ION MOBILITY WORKFLOW
Method for precursor identification from mass spectroscopic data as a function of mass to charge ratio, retention time as well as of ion mobility, using a database of reference precursor data for retrieval of a region of interest for at least three reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension. In a first step for at least three reference precursors, from the database, said data is analysed in the precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension is determined and an ion mobility extraction width window is determined, and in a second step for the identification of further peptide precursors, said extraction width window is used.
The present invention relates to methods for the determination of the residence time between at least one Target and at least one Ligand, optionally in their native biological context, using limited proteolysis e.g., combined with selected reaction monitoring, parallel reaction monitoring, data-independent acquisition (DIA), including Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH) methods and the like.
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
G01N 33/557 - ImmunoassayBiospecific binding assayMaterials therefor using kinetic measurement, i.e. time rate of progress of an antigen-antibody interaction
11.
SYSTEM AND METHOD FOR OPTIMIZING ANALYSIS OF DIA DATA BY COMBINING SPECTRUM-CENTRIC WITH PEPTIDE-CENTRIC ANALYSIS
A method for performing library-free search analysis comprising: performing a search using a spectrum-centric approach (404) for a data (402); performing at least one, preferably both of improving peptide centric analysis of an already optimized or unoptimized predicted spectral library by using the results of said spectrum centric search, preferably in an iterative peptide centric search, for creating a sub-selection of precursors from the optimized or unoptimized predicted spectral library, including a calibration (406) by using results from said spectrum-centric approach; creating an optimized predicted library (409) by refining static prediction models (408a) by using the results of said spectrum-centric approach (404); using said calibration (406) and/or said optimized predicted library (409) to initiate a peptidecentric search (411) for said data (402) based on an in-silico library (409); creating a curated library (412) by combining the results of the spectrum-centric approach (404) with the results from the peptide-centric approach (412); and analyzing the results of the curated library (412) using a second, preferably quantitative, peptide-centric search (413) of the data (402).
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
38 - Telecommunications services
41 - Education, entertainment, sporting and cultural services
42 - Scientific, technological and industrial services, research and design
Goods & Services
Downloadable computer software using artificial intelligence for medical and scientific research, consultation, collection and analysis of data in the field of proteomics research; downloadable artificial intelligence and machine learning software for controlling, tracking, recording and interpreting data relating to proteomics; downloadable bioinformatics workflow management software in the field of proteomics; downloadable software for tracing out biological diagrams in the field of proteomics; downloadable software applications for medical and scientific research, consultation and analysis of data for use with any mass spectrometry proteomics application; downloadable computer software intended for collecting, mining, searching, extracting, managing, analyzing, distributing, sharing and viewing data; downloadable software for accessing computerized data used in the field of proteomics; downloadable software for collaborating and reporting on shared computerized data, and viewing of graphical information, used in the field of proteomics; downloadable software for viewing and analyzing data; downloadable software for data mining in the field of proteomics; downloadable diagnostic software for use in scientific analysis of proteins not for medical use; downloadable software for analyzing proteins, proteomes and biological data; downloadable software for accessing databases and information for research and development services in the fields of medicine, proteomics and biotechnology on a blockchain; downloadable software for the automated mining of proteomic data; downloadable interactive database software for use in database management; downloadable database management software in the field of proteomics; downloadable software for scientific data analysis; recorded or downloadable computer software for use in analyzing data sets in the field of proteomics; downloadable software being scientific devices, namley, downloadable software as a medical device (SaMD) for diagnosing and treating diseases; downloadable data management software for use in the study of proteins and peptides in the development of medicines and pharmaceuticals; downloadable computer databases in the field of proteomics; downloadable interactive databases in the field of proteomics; intelligent gateways being routers in the nature of computer control hardware for real-time data analysis; downloadable software platforms for use in database management in the field of proteomics; downloadable software applications platform using artificial intelligence for preserving and viewing data in the field of proteomics; downloadable information processing systems software using artificial intelligence for use in proteomic analysis; downloadable software platforms, network communication devices, namely, downloadable computer networking software in the nature of mobile applications enabling users to analyze and mining proteomic data; downloadable electronic publications in the nature of journals, scientific posters and research papers in the field of proteomics; downloadable electronic publications transmitted by electronic means, namely, reports, directories and reference materials concerning science. Data processing services and business management services in the fields of science and medicine; management and compilation of computerised databases in the field of proteomics; data processing services in the scientific and medical field; database management for others of a database comprised of proteomic data collected from computerised databases; business advice on database management of proteomic data; data compiling and analyzing statistics, data and other sources of scientific information; compilation of statistical data for use in scientific research, namely,management and compilation of computerised databases Providing an online forum for users for the sharing of data and ideas in the field of proteomics; transmitting and distributing data via a global computer network or via the Internet; providing multiple-user access to the Internet and rental of access time to global computer networks; provision of access to electronic sites, local area computer networks, computer programmes in data networks, a global computer network and the Internet; consulting services relating to data transmission and communication Online publication of specialized journals containing information connected with the use of software in the fields of scientific data management and analysis; non-downloadable electronic publication services in the nature of newsletters, specialized journals and articles, available via a website, in the field of protein data management and protein data analysis; training and online training services, namely, workshops, seminars, webinars, lectures, tutorials in the use and operation of computer software programs in the field of protein data management and protein data analysis; education services, namely, providing education courses in the field of proteomics offered through online, non-downloadable videos and instructor assistance Providing medical and scientific research information in the field of pharmaceuticals and clinical trials based on protein analysis; research services in the field of proteins, antibodies, micro-organisms and cells using proteomics technology; product development advice for inventors in the field of cellular biology using proteomics; technical research and consulting in the pharmaceutical, medical, biological and clinical fields using proteomics technology; providing medical and scientific research information in the pharmaceutical, medical, biological and clinical fields using proteomics technology; medical and scientific research using bioinformatics, namely, proteomics, proteome studies, proteome design, analysis and identification of peptides and proteins, and mass spectrometry; development of pharmaceuticals using proteomics; scientific research and analysis in the field of proteomics conducted using databases; technical data analysis services in the field of proteomics; providing information on clinical studies in the field of proteomics via an interactive website; computer-aided scientific and industrial research analysis services in the field of proteomics; medical and scientific research into the detection of proteins and peptides; biostatistics research services connected with data science; pharmaceutical product discovery and development services; interpreting biological study data, namely, biological research and analysis; providing a website obtaining articles, data sheets, infographics, in the field of proteomics, namely, compiling data for medical and scientific research purposes in the field of proteomics; computer services, namely, providing temporary use of online non-downloadable software for consulting and analyzing scientific information on proteins in the fields of pharmaceutical, biological and clinical sciences; research, design, development, maintenance and support of computer software for scientific data; design services for scientific data processing tools; designing and developing artificial intelligence and machine learning software; software as a service (SaaS) services featuring software for Internet access and for retrieving, managing, analyzing, sharing, collaborating, and reporting computerized data as well as viewing graphic information, used in the fields of protein data management and protein data analysis; providing online non-downloadable computer software for collecting and analysis of data for the purpose of protein data mining; providing online non-downloadable software for database management; temporary provision of online non-downloadable software for importing and managing data; providing temporary use of non-downloadable software for analyzing proteins, proteomes, and biological data; providing temporary use of non-downloadable software for graphical representation of proteomes for use in the development of pharmaceuticals; providing temporary use of non-downloadable software for Internet access and for accessing databases and information intended for research and development services in the fields of proteomics and biotechnology; providing online non-downloadable software for enabling scientists and clinicians to interactively manage and share proteomic data; providing temporary use of non-downloadable software for analyzing scientific data and generating reports; biobank services, namely, electronic data storage and analysis of biological, clinical, chemical, forensic and biopharmaceutical substances and samples in a database for scientific purposes; providing online non-downloadable information processing system software using artificial intelligence for proteomic analysis; software as a service with intelligent gateways in the nature of non-downloadable software for use in data analysis in the field of proteomics; proteomic life sciences computer platform as a service [PaaS] featuring computer software platforms for database management; development of computer platforms; software as a service [SaaS] services featuring software using artificial intelligence for preserving and viewing data in the field of proteomics; Platform as a service (PaaS) featuring computer software platforms for accessing databases, extracting, managing, analyzing, sharing, collaborating, and reporting computerized data and viewing graphic information, for use in the field of proteomics; providing online non-downloadable software and software platform for accessing databases data and services related to proteomics; providing online non-downloadable software platforms for providing data reports and appraisals in the field of proteomics; computer platform as a service (PaaS) featuring software platforms for use in database management and analysis of proteomic data for the discovery and development of new drugs; electronic storage of data in a data warehouse; data mining; medical and scientific research, namely, analyzing proteomic data; medical and scientific advice on the analysis of proteomic data.
13.
METHOD AND TOOLS FOR THE DETERMINATION OF CONFORMATIONS AND CONFORMATIONAL CHANGES OF PROTEINS AND OF DERIVATIVES THEREOF
Method for the detection of a conformational state of a protein, said protein being in a complex mixture of further proteins and other biomolecules, wherein the protein in said complex mixture has been subjected to a condition inducing a structural change in said the protein, comprising the following sequence of steps: 1. Limited proteolysis of the extract mixture under a condition in which the protein is in the original conformational state to be detected leading to a first fragment sample; directly followed by 2. Removal of large peptides and proteins or other biomolecules from said first fragment sample to form an enriched fragment sample; 3. Analytical analysis of the enriched fragment sample for the determination of fragments characteristic of having been the result of the limited proteolysis of step 1. as well as remaining after the removal step 2. for the determination of the conformational state of said at least one protein.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Devices for analyzing protein sequences used as laboratory
apparatus; pharmaceutical and scientific research equipment
for use in mass spectrometers based proteomics; downloadable
computer software using artificial intelligence in the field
of proteomics research; proteomic research laboratory
analyzers for measuring, testing and analyzing blood and
other bodily protein fluids; imaging apparatus and
instruments for use in the study of proteins and peptides in
drug development; apparatus and instruments for mass
spectrometry based proteomics; downloadable workflow
management software for bioinformatics in the field of
proteomics; scientific apparatus, namely, spectrophotometer
for measuring relative DNA, RNA and protein quantities;
downloadable biology diagramming software in the field of
proteomics; downloadable software applications for any
application of mass spectrometry in the field of proteomics. Providing medical and scientific research information in the
field of pharmaceuticals and clinical trials based on
protein analysis; Pharmaceutical drug development services
using proteomics; life science proteomics platform as a
service [PaaS]; research services in the field of proteins,
antibodies, microorganisms and cells using proteomics
technology; cell culture services for scientific and
research purposes for others using proteomics technology;
product development consultancy for inventors in the field
of cellular biology using proteomics; technical research and
consultation in the fields of pharmaceuticals, medicine,
biological and clinical sciences using proteomic technology;
providing medical and scientific research information in the
fields of pharmaceuticals, medicine, biological and clinical
sciences using proteomic technology; computer services,
namely temporary provision of non-downloadable software
online for consultation and analysis of scientific
information on proteins in the fields of pharmaceutical,
biological and clinical sciences; medical and scientific
research using bioinformatics, namely, proteomics, proteome
studies, proteome designs, peptide and protein analysis and
identification, mass spectrometry; scientific laboratory
services in the field of proteomics; conducting clinical
trials for others [scientific research] based on protein
analysis.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Devices for analyzing protein sequences used as laboratory
apparatus; pharmaceutical and scientific research equipment
for use in mass spectrometers based proteomics; downloadable
computer software using artificial intelligence in the field
of proteomics research; proteomic research laboratory
analyzers for measuring, testing and analyzing blood and
other bodily protein fluids; imaging apparatus and
instruments for use in the study of proteins and peptides in
drug development; apparatus and instruments for mass
spectrometry based proteomics; downloadable workflow
management software for bioinformatics in the field of
proteomics; scientific apparatus, namely, spectrophotometer
for measuring relative DNA, RNA and protein quantities;
downloadable biology diagramming software in the field of
proteomics; downloadable software applications for any
application of mass spectrometry in the field of proteomics. Providing medical and scientific research information in the
field of pharmaceuticals and clinical trials based on
protein analysis; Pharmaceutical drug development services
using proteomics; life science proteomics platform as a
service [PaaS]; research services in the field of proteins,
antibodies, microorganisms and cells using proteomics
technology; cell culture services for scientific and
research purposes for others using proteomics technology;
product development consultancy for inventors in the field
of cellular biology using proteomics; technical research and
consultation in the fields of pharmaceuticals, medicine,
biological and clinical sciences using proteomic technology;
providing medical and scientific research information in the
fields of pharmaceuticals, medicine, biological and clinical
sciences using proteomic technology; computer services,
namely temporary provision of non-downloadable software
online for consultation and analysis of scientific
information on proteins in the fields of pharmaceutical,
biological and clinical sciences; medical and scientific
research using bioinformatics, namely, proteomics, proteome
studies, proteome designs, peptide and protein analysis and
identification, mass spectrometry; scientific laboratory
services in the field of proteomics; conducting clinical
trials for others [scientific research] based on protein
analysis.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Devices for analyzing protein sequences and serving as
laboratory apparatus; pharmaceutical and scientific research
apparatus for proteomics based on mass spectrometers;
downloadable computer software using artificial intelligence
in the field of proteomics research; proteomics research
laboratory analyzers for measuring, testing and analyzing
blood and other body protein fluids; imaging apparatus and
instruments for the study of proteins and peptides in the
development of pharmaceuticals; apparatus and instruments
for proteomics based on mass spectrometry; downloadable
bio-informatics workflow management software in the field of
proteomics; scientific apparatus, namely, a
spectrophotometer to measure the relative quantities of DNA,
RNA and protein; downloadable software for tracing out
biological diagrams in the field of proteomics; downloadable
software applications for any mass spectrometry proteomics
application. Providing medical and scientific research information in the
field of pharmaceuticals and clinical trials based on
protein analysis; development of pharmaceuticals using
proteomics; proteomic life sciences computer platform as a
service [PaaS]; research services in the field of proteins,
antibodies, micro-organisms and cells using proteomics
technology; cell culture services for scientific and
research purposes for others using proteomics technology;
product development advice for inventors in the field of
cellular biology using proteomics; technical research and
consulting in the pharmaceutical, medical, biological and
clinical fields using proteomics technology; providing
medical and scientific research information in the
pharmaceutical, medical, biological and clinical fields
using proteomics technology; computer services, namely,
providing temporary use of online non-downloadable software
for consulting and analyzing scientific information on
proteins in the fields of pharmaceutical, biological and
clinical sciences; medical and scientific research using
bio-informatics, namely, proteomics, proteome studies,
proteome design, analysis and identification of peptides and
proteins, mass spectrometry; scientific laboratory services
in the field of proteomics; conducting clinical tests for
others [scientific research] based on protein analysis.
17.
SYSTEM AND METHOD FOR IMPROVING HIGH-PRECISION ION MOBILITY WORKFLOW
Method for the targeted peptide precursor identification from sample mass spectroscopic intensity data acquired as a function of mass to charge ratio (m/z), of retention time (RT) as well as of ion mobility (IM), using a database of reference peptide precursor data for retrieval of a region of interest for at least three reference peptide precursors in the mass to charge ratio (m/z), the retention time (RT) as well as in the ion mobility (IM) dimension. For peptide precursor identification from the sample mass spectroscopic intensity data, in a first step for at least three reference peptide precursors, preferably for all reference peptide precursors from the database of reference peptide precursor data, said sample mass spectroscopic intensity data is analysed in the respective reference peptide precursor region of interest of mass to charge ratio (m/z), retention time (RT) as well as ion mobility (IM) dimension, and from that analysis empirically an adjusted center in the ion mobility dimension (IM) for each reference peptide precursor is determined and an ion mobility extraction width window in the ion mobility dimension (IM), preferably as a variable function of the ion mobility dimension (IM), is determined, and in a second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined ion mobility extraction width window in the ion mobility dimension (IM), preferably as a variable function of the ion mobility dimension (IM) is used.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Laboratory apparatus for analyzing protein sequences; pharmaceutical and scientific research apparatus for proteomics based on mass spectrometers; downloadable computer software using artificial intelligence in the field of proteomics research; proteomics research laboratory analyzers for measuring, testing and analyzing blood and other body protein fluids; imaging apparatus and instruments for the study of proteins and peptides in the development of pharmaceuticals; apparatus and instruments for proteomics based on mass spectrometry; downloadable bio-informatics workflow management software in the field of proteomics; scientific apparatus, namely, a spectrophotometer to measure the relative quantities of DNA, RNA and protein; downloadable software for tracing out biological diagrams in the field of proteomics; downloadable software applications for any mass spectrometry proteomics application Providing medical and scientific research information in the field of pharmaceuticals and clinical trials based on protein analysis; development of pharmaceuticals using proteomics; platform as a service (PaaS) featuring software for analyzing protein sequences in the field of life science proteomics; research services in the field of proteins, antibodies, micro-organisms and cells using proteomics technology; cell culture services for scientific and research purposes for others using proteomics technology; product development advice for inventors in the field of cellular biology using proteomics; technical research and consulting in the pharmaceutical, medical, biological and clinical fields using proteomics technology; providing medical and scientific research information in the pharmaceutical, medical, biological and clinical fields using proteomics technology; computer services, namely, providing temporary use of non-downloadable software for consulting and analyzing scientific information on proteins in the fields of pharmaceutical, biological and clinical sciences; medical and scientific research using bio-informatics, namely, proteomics, proteome studies, proteome design, analysis and identification of peptides and proteins, mass spectrometry; scientific laboratory services in the field of proteomics; conducting clinical trials for others in the nature of scientific research based on protein analysis
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Laboratory apparatus for analyzing protein sequences; pharmaceutical and scientific research equipment for use in mass spectrometers based proteomics; downloadable computer software using artificial intelligence in the field of proteomics research; proteomic research laboratory analyzers for measuring, testing and analyzing blood and other bodily protein fluids; imaging apparatus and instruments for use in the study of proteins and peptides in drug development; apparatus and instruments for mass spectrometry based proteomics; downloadable workflow management software for bioinformatics in the field of proteomics; scientific apparatus, namely, spectrophotometer for measuring relative DNA, RNA and protein quantities; downloadable biology diagramming software in the field of proteomics; downloadable software applications for any application of mass spectrometry in the field of proteomics Providing medical and scientific research information in the field of pharmaceuticals and clinical trials based on protein analysis; Pharmaceutical drug development services using proteomics; platform as a service (PaaS) featuring software for analyzing protein sequences in the field of life science proteomics; research services in the field of proteins, antibodies, microorganisms and cells using proteomics technology; cell culture services for scientific and research purposes for others using proteomics technology; product development consultancy for inventors in the field of cellular biology using proteomics; technical research and consultation in the fields of pharmaceuticals, medicine, biological and clinical sciences using proteomic technology; providing medical and scientific research information in the fields of pharmaceuticals, medicine, biological and clinical sciences using proteomic technology; computer services, namely, providing temporary use of non-downloadable software online for consultation and analysis of scientific information on proteins in the fields of pharmaceutical, biological and clinical sciences; medical and scientific research using bioinformatics, namely, proteomics, proteome studies, proteome designs, peptide and protein analysis and identification, mass spectrometry; scientific laboratory services in the field of proteomics; conducting clinical trials for others in the nature of scientific reseach based on protein analysis
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Laboratory apparatus for analyzing protein sequences; pharmaceutical and scientific research equipment for use in mass spectrometers based proteomics; downloadable computer software using artificial intelligence in the field of proteomics research; proteomic research laboratory analyzers for measuring, testing and analyzing blood and other bodily protein fluids; imaging apparatus and instruments for use in the study of proteins and peptides in drug development; apparatus and instruments for mass spectrometry based proteomics; downloadable workflow management software for bioinformatics in the field of proteomics; scientific apparatus, namely, spectrophotometer for measuring relative DNA, RNA and protein quantities; downloadable biology diagramming software in the field of proteomics; downloadable software applications for any application of mass spectrometry in the field of proteomics Providing medical and scientific research information in the field of pharmaceuticals and clinical trials based on protein analysis; Pharmaceutical drug development services using proteomics; platform as a service (PaaS) featuring software for analyzing protein sequences in the field of life science proteomics; research services in the field of proteins, antibodies, microorganisms and cells using proteomics technology; cell culture services for scientific and research purposes for others using proteomics technology; product development consultancy for inventors in the field of cellular biology using proteomics; technical research and consultation in the fields of pharmaceuticals, medicine, biological and clinical sciences using proteomic technology; providing medical and scientific research information in the fields of pharmaceuticals, medicine, biological and clinical sciences using proteomic technology; computer services, namely,providing temporary use of non-downloadable software online for consultation and analysis of scientific information on proteins in the fields of pharmaceutical, biological and clinical sciences; medical and scientific research using bioinformatics, namely, proteomics, proteome studies, proteome designs, peptide and protein analysis and identification, mass spectrometry; scientific laboratory services in the field of proteomics; conducting clinical trials for others in the nature of scientific research based on protein analysis
21.
Labelled compounds and methods for mass spectrometry-based quantification
Methods for peptide and/or protein quantification by mass spectrometry using labeled peptides, wherein multiple labels lead to distinct fragments for the labeled peptides and their unlabeled variant, thus facilitating data analysis and enhancing the potential for quantification. Methods for selecting the label and label position are further given, as well as sets of labeled peptides resulting from or for use in the above-mentioned methods. The methods and substances are especially useful for data-independent or multiplexed parallel reaction monitoring proteomics applications involving peptide quantification.
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological services as well as research
and design services relating thereto; industrial analysis
and research services; design and development of computers
and software.
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological services as well as research
and design services relating thereto; industrial analysis
and research services; design and development of computers
and software.
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological applications and services as well as research applications and services relating thereto, namely, research and development in the biotechnology and life science field and custom design and development of biochemical assays; industrial analysis and research applications and services, namely, analysis and research in the pharmacological and clinical field, in particular proteomic, molecular, genetic and medical analysis and research; analysis of data in the fields of proteomic, molecular, genetic and medical research; development of software
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological applications and services as well as research applications and services relating thereto, namely, research and development in the biotechnology and life science field and custom design and development of biochemical assays; industrial analysis and research applications and services, namely, analysis and research in the pharmacological and clinical field; analysis of data; development of software and data analysis workflows
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological services as well as research
and design services relating thereto; industrial analysis
and research services; design and development of computers
and software.
42 - Scientific, technological and industrial services, research and design
Goods & Services
Scientific and technological services as well as research and design services relating thereto, namely, research services in the field of pharmaceutical products and biotechnology and clinical development of pharmaceuticals; industrial analysis and research services in the field of mass spectrometry and life sciences namely, in biology, proteomics, pharmacology, genomics, pharmacogenomics, medical device, biotechnology, genetics, molecular biology, bioinformatics, biochemistry, immunotherapy, immunology, oncology and neurosciences; Design and development of software
28.
Labelled compounds and methods for mass spectrometry-based quantification
Methods for peptide and/or protein quantification by mass spectrometry using labeled peptides, wherein multiple labels lead to distinct fragments for the labeled peptides and their unlabeled variant, thus facilitating data analysis and enhancing the potential for quantification. Methods for selecting the label and label position are further given, as well as sets of labeled peptides resulting from or for use in the above-mentioned methods. The methods and substances are especially useful for data-independent or multiplexed parallel reaction monitoring proteomics applications involving peptide quantification.
The invention relates to methods for peptide and/or protein quantification by mass spectrometry using labeled peptides, wherein multiple labels lead to distinct fragments for the labeled peptides of the present invention and their unlabeled variant, thus facilitating data analysis and enhancing the potential for quantification. In further aspects the present invention relates to methods for selecting the label and label position. In even further aspects the present invention relates to sets of labeled peptides resulting from or for use in the above-mentioned methods. It is contemplated that the methods and substances of the invention will be especially useful for data-independent or multiplexed parallel reaction monitoring proteomics applications involving peptide quantification. A reference peptide is used in these methods, which is selectively isotopically labeled by having incorporated one isotopically labeled amino acid forming its very C-terminus or being one of the four terminal amino acids at the C-terminus and additionally one further isotopically labeled amino acid forming its very N-terminus, or being one of the four terminal amino acids at the N-terminus.
A method of the analysis of compounds with mass spectrometry and to instruments, substances, and methods for polypeptide analysis, in particular in targeted proteomics applications and based on indexed retention times as peptide specific property. The method of chemical analysis comprises the steps of: a) providing a first sample comprising peptides; b) performing LC-MS and determining the empirical retention time values of the peptides; c) translating the empirical retention time values into the indexed retention time scale and associating a reference indexed retention time value; d) providing a second complex sample comprising peptides; e) performing LC-MS and determining the empirical retention time values; f) translating the empirical retention time values of the peptides into the indexed retention time scale by numerically adapting the transformation function; and g) determining the predicted empirical retention time value of the peptides by using the numerically adapted transformation function determined in step f).
The invention relates to the analysis of compounds with mass spectrometry and more particularly to instruments, substances, and methods for polypeptide analysis, in particular in targeted proteomics applications and based on indexed retention time as peptide specific property. The method of chemical analysis comprises the steps of: a) providing a first complex sample comprising a set of at least two reference peptides associated to an indexed retention time scale (iRT), as well as at least one further peptide; b) performing LC-MS on said complex sample and determining the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide; c) translating the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide into the indexed retention time scale and associating to each reference peptide a reference indexed retention time value (iRTr) and to the at least one further peptide an associated indexed retention time value (iRTa); d) providing a second complex sample comprising at least one polypeptide as well as said set of the at least two reference peptides; e) performing LC-MS on said second complex sample and determining the empirical retention time values (RTe) of the reference peptides; f) translating the empirical retention time values (RTe) of the reference peptides into the indexed retention time scale by numerically adapting the transformation function for the conversion of the retention time values (RTe) into indexed retention time values such that the calculated indexed retention time values (iRTe) calculated based on the measured retention time values (RTe) of the reference peptides match the assigned indexed retention time values (iRTr) of the reference peptides; g) determining the predicted empirical retention time value (RTp) of the at least one further peptide by using the numerically adapted transformation function determined in step f).
