Abstract

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.

IPC Classes  ?

• G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
• G16B 15/30 - Drug targeting using structural dataDocking or binding prediction
• G16B 35/10 - Design of libraries
• G16B 40/20 - Supervised data analysis

Abstract

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.

IPC Classes  ?

• G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids

Abstract

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.

IPC Classes  ?

• G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
• G01N 30/72 - Mass spectrometers
• G01N 30/88 - Integrated analysis systems specially adapted therefor, not covered by a single one of groups

Abstract

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.

IPC Classes  ?

• G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids

Abstract

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.

IPC Classes  ?

• G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids

Abstract

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).

IPC Classes  ?

• G01N 30/86 - Signal analysis
• G01N 30/88 - Integrated analysis systems specially adapted therefor, not covered by a single one of groups
• G01N 30/04 - Preparation or injection of sample to be analysed