Eth Zurich

Dh Technologies Development Pte. Ltd.

Institute for Systems Biology

Kantonsspital St. Gallen

Eidgenossische Technische Hochschule Zurich

Rudolf Aebersold

Oliver Rinner

Stephen Alexander Tate

Ronald Francis Bonner

Lukas Reiter

Pedro Jose Navarro Alvarez

Ludovic Gillet

Bernd Wollscheid

Dan Martin

Julian Watts

Silke Gillessen

Ralph Schiess

Wilhelm Krek

Igor Cima

Thomas Cerny

Hamid Mirzaei

Paola Picotti

Johan Malmstroem

Systems and methods are disclosed for analyzing a sample using overlapping precursor isolation windows. A mass analyzer of a tandem mass spectrometer is instructed to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor. The tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.

Data independent acquisition of product ion spectra and reference spectra library matching

The invention relates to biomarker assays based on protein/peptide biomarkers which show a pronounced differential behaviour between healthy and cancerous sample proteomes e.g. by mass spectrometric measurement and/or antibody-based assays such as an Enzyme-Linked Immunosorbent Assay (ELISA) determination of the protein biomarkers in serum, plasma or blood itself.

Method for biomarker and drug-target discovery for prostate cancer diagnosis and treatment as well as biomarker assays determined therewith

The invention relates to a method for the determination of a cancer diagnostic/therapeutic biomarker assay and drug-targets including the following steps: (a) identification of potential candidate protein/peptide biomarkers and drug-targets based on the measurement of protein/peptide constituent concentrations in tissue sample proteomes as well as serum, plasma or any other derivatives of blood, or blood itself sample proteomes derived from healthy non-human mammalian individuals as well as from cancerous non-human mammalian individuals and qualitatively selecting as potential candidate protein/peptide biomarkers those which show a pronounced differential behavior between healthy and cancerous sample proteomes; (b) optional verification of the potential candidate protein/peptide biomarkers as identified in step (a) by quantitative mass spectrometric measurement of the potential candidate protein biomarkers in serum, plasma or any other derivatives of blood, or blood itself sample proteomes derived from healthy non-human mammalian individuals as well as from cancerous non-human mammalian individuals and selecting as candidate protein/peptide biomarkers those which show a mass-spectrometrically measurable quantitative differential behavior between healthy and cancerous sample proteomes; (c) validation of the candidate protein/peptide biomarkers as identified in step (a), or as optionally verified in step (b), by mass spectrometric measurement and/or antibody-based assays such as an Enzyme-Linked Immunosorbent Assay (ELISA) determination of the candidate protein biomarkers in serum, plasma or any other derivatives of blood, or blood itself sample proteomes derived from healthy human individuals as well as from cancerous human individuals and selecting as protein/peptide biomarkers those which show a mass-spectrometrically measurable and/or antibody-based assay detectable differential behavior between healthy and cancerous sample proteomes; (d) application of statistical methods to uncover single or groups of protein/peptide biomarkers as validated in step (c) as signatures for the detection of patients with cancer. The invention furthermore relates to specific biomarker assays for the highly reliable diagnosis of cancer, specifically of localized or non-localized prostate cancer, using human serum, plasma or any other derivatives of blood, or blood itself.

Systems and methods are disclosed for quantitating detectable compounds of a sample. Sample product ion spectra are received for each mass selection window for each time step. The received sample product ion spectra are searched for the presence of known compounds of interest with known product ion spectra by retrieving the known product ion spectra from a library, retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra, generating product ion traces in time for the sample product ion spectra for the known product ion spectra, calculating a score for the product ion traces and product ion spectra that represents how well known product ions and sample product ions match, and calculating a quantitative value for the known compound from the product ion traces when the score exceeds a threshold value.

Systems and methods are disclosed for identifying detectable compounds of a sample. Sample product ion spectra are received for each mass selection window of precursor mass selection windows for each time step. The received sample product ion spectra are searched for the presence of known compounds of interest with known product ion spectra by retrieving a known product ion spectrum from a library, retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectrum, generating product ion traces in time for the retrieved sample product ion spectra, calculating a score for the product ion traces and the retrieved sample product ion spectra that represents how well the retrieved sample product ion spectra and the known product ion spectrum match, and confirming the identity of a precursor ion using the score.

Systems and methods are used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.

Methods of using halogenated peptides as internal standards for liquid chromatography-mass spectrometry, and novel halogenated peptides useful for the same, are disclosed. In particular, methods of using halogenated peptides as internal standards in proteomic analyzes, as well as methods of using halogenated peptides to conduct quality control assessments of and/or to calibrate liquid chromatography-mass spectrometry systems are disclosed.

Methods of using halogenated peptides as internal standards for liquid chromatography-mass spectrometry

The invention relates to a method for the determination of an MRM or SRM assay for a protein of interest, a peptide of interest, or a group of proteins/peptides of interest or a whole proteome. It essentially includes the following steps: (1) a list of proteins of interest is selected and for each member at least one or a list of candidate proteotypic peptides is derived (2) this at least one peptide is synthesized/generated essentially without subsequent purification; (3) this at least one unpurified peptide is analyzed by selected reaction monitoring (SRM) preferably coupled to liquid chromatography (LC-SRM) or analogous techniques; (4) validation and/or optimisation of the corresponding assay of the at least one peptide with determination of the SRM coordinates for a peptide/protein of interest and/or of a regulator of interest is achieved. A protein sample of interest is enzymatically digested and can then be analyzed in SRM mode or time-constrained SRM mode, using elution times to trigger acquisition of the set of selected SRM traces, thus drastically increasing the throughput. The analysis allows to detect and quantify the set of peptides/proteins of interest. The method additionally relates to a tagging strategy to achieve absolute quantification of the peptides/proteins of interest at low-budget and high-throughput.

Method for high throughput peptide/protein assay generation and assays generated therewith

Methods of using halogenated peptides as internal standards for liquid chromatography-mass spectrometry, and novel halogenated peptides useful for the same, are disclosed. In particular, methods of using halogenated peptides as internal standards in proteomic analyses, as well as methods of using halogenated peptides to conduct quality control assessments of and/or to calibrate liquid chromatography-mass spectrometry systems are disclosed.

The invention provides methods for preparing a peptide as an immunogen to generate an antibody specific for the deglycosylated form of a glycopolypeptide by preparing a peptide that includes an N-linked glycosylation site of said glycopolypeptide and identifying a peptide sequence that includes said glycosylated site and preparing said peptide wherein N of said site is converted to D.

Methods for characterizing glycoproteins and generating antibodies for same

The invention provides methods for preparing a peptide useful in generating an antibody specific for the glycosylated form of a glycopolypeptide wherein the glycosylated portion is isolated and a peptide corresponding to amino acids adjacent to a glycosylated N-linked glycosylation site is prepared.

The invention provides methods for generating an antibody specific for the deglycosylated form of a glycopolypeptide using a peptide corresponding to an N-linked glycosylation site of a glycopolypeptide. The invention additionally provides methods for generating an antibody specific for a glycopolypeptide using a peptide corresponding to amino acids adjacent to an authentic N-linked glycosylation site.

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Zurich, Switzerland

Rudolf Aebersold