Data Processing Device and Method for the Evaluation of Mass Spectrometry Data

Abstract

A data processing device comprises a processor unit adapted to process a plurality of initial data vectors provided by a chromatograph and/or a mass spectrometer, the processing being carried out in one, two or more processing steps producing items of processed data, and a storage unit adapted to save and retrieve initial data vectors and/or items of processed data, in particular processed data vectors or identified compounds, and/or items of additional data, in particular properties of the sample introduced in the mass spectrometer. Each item of processed data and/or additional data is connected to at least one initial data vector, and wherein the processor unit is adapted to group, select and/or modify initial data vectors and/or items of processed data according to one or more items of additional data.

1 . A data processing device, comprising a processor unit adapted to process a plurality of initial data vectors provided by a chromatograph and/or a mass spectrometer, the processing being carried out in one, two or more processing steps producing items of processed data, and a storage unit adapted to save and retrieve initial data vectors and/or items of processed data, in particular processed data vectors or identified compounds, and/or items of additional data, in particular properties of the sample introduced in the mass spectrometer, wherein each item of processed data and/or additional data is connected to at least one initial data vector, and wherein the processor unit is adapted to group, select and/or modify initial data vectors and/or items of processed data according to one or more items of additional data. 
     
     
         2 . The data processing device of  claim 1 , wherein each initial data vector is assigned a unique identifier, and wherein each item of processed data is connected to an item of processed data from a preceding processing step of the same initial data vector and/or directly to the initial data vector. 
     
     
         3 . The data processing device of  claim 1 , wherein the storage unit is adapted to store the initial data vectors, the items of processed data and/or the items of additional data in a relational database. 
     
     
         4 . The data processing device of  claim 3 , wherein the relational database comprises a fixed number of predefined tables and a number of dynamic tables, wherein at least one of the predefined tables contains a definition of dynamic data types, and wherein one dynamic table is created for each dynamic data type. 
     
     
         5 . The data processing device of  claim 4 , wherein the storage unit comprises a data interface for defining dynamic data types and/or modifying the relational database, so that dynamic tables can be added and/or columns can be added to existing dynamic tables. 
     
     
         6 . The data processing device of  claim 4 , wherein the definition of dynamic data types may comprise references to converters, wherein a storage form of an item of the defined dynamic data type is converted into a processing form when retrieving data from the storage unit, and the processing form of an item of the defined dynamic data type is converted into the storage form when saving data to the storage unit. 
     
     
         7 . The data processing device of  claim 4 , wherein the storage unit is adapted to store connections between items of a first and items of a second dynamic data type, and wherein the relational database comprises at least one further dynamic table containing the connections between the items of the first and the items of the second dynamic data type. 
     
     
         8 . The data processing device of  claim 7 , wherein one dynamic table is created for each connection between two dynamic data types, and wherein the dynamic table of a connection contains one or more columns for storing items of additional data and/or items of processed data. 
     
     
         9 . The data processing device of  claim 4 , wherein at least one of the dynamic data types is adapted for the characterization of the sample and/or the targeted compound. 
     
     
         10 . The data processing device of  claim 9 , wherein the samples introduced in the mass spectrometer contain proteins and/or peptides, in particular digested proteins, wherein the dynamic data types comprise protein, in particular comprising a sequence and a description and a weight, and peptide, in particular comprising a sequence and a charge, wherein the processing comprises a processing step of identifying peptides and a subsequent processing step of identifying proteins, and wherein the relational database comprises a table of identified proteins and a table of identified peptides. 
     
     
         11 . The data processing device of  claim 9 , wherein the samples introduced in the mass spectrometer contain a drug and/or a metabolite, wherein the user-defined data types comprise drug, in particular comprising name, period of effect and tissue of the sample, metabolite, in particular comprising chemical formula and/or name, and modification, in particular comprising charge, mass and position wherein the processing preferably comprises a processing step of identifying metabolites. 
     
     
         12 . The data processing device of  claim 4 , further comprising a module interface, which allows for adding dynamic modules that implement processing steps, wherein the dynamic modules can save and/or retrieve items of data as well as add dynamic data types and/or modify tables of the relational database. 
     
     
         13 . The data processing device of  claim 12 , the data processing device further comprising a workflow interface for defining sequences of processing steps, wherein processing steps can be performed by default modules and/or dynamic modules, wherein the workflow interface provides services to modules which allows them to retrieve data from the relational database, define dynamic data types, and to save data in the relational database. 
     
     
         14 . The data processing device of  claim 13 , wherein the workflow interface is adapted to define a first and a second workflow, each workflow comprising a sequence of one or more processing steps, wherein the first workflow is carried out by the processor unit before the second workflow, and wherein the processed data from the first workflow is used as input data for the second workflow. 
     
     
         15 . The data processing device of  claim 14 , wherein the workflow interface is adapted to define a number of first workflows, each workflow comprising a sequence of one or more processing steps, wherein the first workflows are carried out independently by the processor unit, and wherein the second workflow comprises a processing step of combining, comparing and/or analyzing the processed data resulting from the number of first workflows. 
     
     
         16 . The data processing device of  claim 12 , wherein the data processing device is adapted to store a workflow comprising a sequence of processing steps in a workflow file, wherein the workflow file preferably comprises a list of initial vectors to be processed, and wherein the data processing device is further adapted to store at least the items of processed data, preferably initial data vectors, items of processed data and items of additional data, from a workflow being carried out by the processor unit in a result file, in particular a relational database file. 
     
     
         17 . The data processing device of  claim 16 , wherein before carrying out a subsequently defined workflow, the processor unit is adapted to compare the processing steps and the list of initial data vectors of the subsequently defined workflow to the processing steps and the list of initial data vectors of one or more stored workflows, and if both the processing steps and the list of initial data files of a stored workflow correspond to the initial processing steps of the subsequent workflow, data from the corresponding result file of that stored workflow is retrieved in place of carrying out the initial processing steps of the subsequently defined workflow. 
     
     
         18 . The data processing device of  claim 12 , wherein the storage unit is further adapted to store for each item of processed data which default or dynamic module created or modified this item of processed data. 
     
     
         19 .- 23 . (canceled) 
     
     
         24 . Method for identifying and/or quantifying peptides and/or proteins and/or metabolites, comprising the steps of
 a. Acquiring initial data vectors of a plurality of samples by a mass spectrometry setup, in particular a mass spectrometry setup according to claim  23 ,   b. Assigning one or more items of additional data to each initial data vector,   c. Grouping or selecting a number of initial data vectors according to an item of additional data, in particular selecting only those initial data vectors for which the item of additional data has a predefined value,   d. Processing the grouped or selected number of initial data vectors in one or more processing steps comprising preferably modifying a mass scale and/or an intensity of the initial data vectors,   e. Performing a search in a database of known mass spectra from peptides and/or proteins and/or metabolites, and   f. Outputting the names and/or properties of the peptides and/or proteins and/or metabolites identified by the database search.   
     
     
         25 . Method according to  claim 24 , further comprising at least one of the steps of
 g. Assigning one or more items of additional data to each item of processed data,   h. Grouping or selecting a number of processed data items according to an item of additional data directly assigned to the processed data item or assigned to an item of processed data from a preceding processing step of the same initial data vector and/or directly to the initial data vector,   i. Processing the grouped or selected number of processed data items in one or more steps preferably comprising a validation of the processed data items,   
       wherein one or more of the steps may be repeated before the final step of outputting the names and/or properties of the peptides and/or proteins and/or metabolites.