Web-Based Data Upload and Visualization Platform Enabling Creation of Code-Free Exploration of MS-Based Omics Data

Abstract

The present invention provides a platform that enables codeless generation of online mass spectrometry data exploration portals. The platform facilitates upload of generic spreadsheets containing processed mass spectrometry results (e.g., peak tables) and enables on-the-fly hierarchical organization of data. Following data upload, platform users can select individual visualizations to add to their custom web portal from a menu of options. Based on these selections, a complete webpage is constructed with all associated functionality embedded. These custom web portals can then be shared with collaborators and other researchers at the discretion of the creator via a developed user permissions sharing scheme.

1 . A computer-implemented method for generating and presenting mass spectrometry (MS) data comprising the steps of:
 a) providing an electronic database across a network to a plurality of users;   b) receiving or generating one or more electronic peak tables comprising MS data;   c) assigning unique numerical identifiers to one or more subsets of said MS data in said one or more electronic peak tables, wherein the unique numerical identifiers identify data contained within the data subsets to be used in statistical analysis;   d) storing said data subsets with unique numerical identifiers in said electronic database;   e) performing statistical analysis of said stored data subsets thereby generating analyzed MS data;   f) providing one or more data visualization options to a user through the network, wherein said one or more visualization options correspond to one or more selectable graphs, charts, tables, or combinations thereof, able to display at least a portion of said analyzed MS data;   g) receiving one or more selected data visualization options from the user; and   h) generating and displaying one or more graphs, charts, tables, or combinations thereof, corresponding to the data visualization options selected by the user, wherein the one or more graphs, charts, tables, or combinations thereof, are generated from the analyzed MS data.   
     
     
         2 . The method of  claim 1  wherein the one or more peak tables are generated by a separate MS software program following one or more MS experiments and include data comprising names of molecules profiled by the one or more MS experiments, mass-to-charge ratios of peaks obtained during the one or more MS experiments, and intensity of peaks obtained during the one or more MS experiments. 
     
     
         3 . The method of  claim 2  wherein the unique numerical identifiers identify the one or more subsets of said MS data corresponding to the molecule names, mass-to-charge ratios, peak intensity, and combinations thereof from the one or more peak tables. 
     
     
         4 . The method of  claim 1  wherein performing statistical analysis of said stored data subsets comprises the step of combining MS obtained from multiple MS experiments. 
     
     
         5 . The method of  claim 1  wherein the steps of storing the data subsets in the electronic database and performing statistical analysis of the stored data subsets are performed automatically. 
     
     
         6 . The method of  claim 1  wherein the one or more visualization options comprise volcano plots, bar charts, scatter plots, and principal component analysis (PCA). 
     
     
         7 . The method of  claim 1  further comprising providing a web portal, wherein the web portal displays the one or more data visualization options to the user and allows the user to select the desired data visualization options. 
     
     
         8 . The method of  claim 7  further comprising providing the generated graphs, charts, tables, or combinations thereof, on the web portal. 
     
     
         9 . The method of  claim 1  further comprising providing restricted access, wherein said restricted access allows an authorized user to view the web portal and download the analyzed MS data. 
     
     
         10 . The method of  claim 9  wherein said restricted access further allows an authorized user to upload MS data to the database using the one or more electronic peak tables, select data visualization options to generate the graphs, charts, tables, or combinations thereof, and to edit and/or remove said MS data. 
     
     
         11 . The method of  claim 9  wherein said restricted access further allows an authorized user the ability to grant collaborating users access to the web portal and electronic database, and the ability to delete the web portal and electronic database entirely. 
     
     
         12 . The method of  claim 1  further comprising the step of assigning organizational identifiers to one or more subsets of said MS data in said one or more electronic peak tables, and storing said data subsets with organizational identifiers in the electronic database. 
     
     
         13 . The method of  claim 12  further comprising generating and displaying one or more graphs, charts, tables, or combinations thereof, from analyzed MS data having the same organizational identifiers separate from analyzed MS data having different organizational identifiers. 
     
     
         14 . The method of  claim 13  further comprising providing a web portal, wherein the web portal displays the available graphs, charts, tables, or combinations thereof, from the analyzed MS data to the user and allows the user to select the desired graphs, charts, tables, or combinations thereof, based on the organizational identifiers. 
     
     
         15 . The method of  claim 14  wherein the organizational identifiers comprise one or more project identifiers, each project identifier able to identify a unique MS project. 
     
     
         16 . The method of  claim 14  wherein the organizational identifiers comprise one or more branch identifiers, each branch identifier able to identify a unique collection of protein, metabolite, or lipid MS data able to be compared in downstream analyses. 
     
     
         17 . The method of  claim 14  wherein the organizational identifiers comprise one or more peak table set identifiers, each peak table set identifier able to identify MS data obtained from the same electronic peak table. 
     
     
         18 . The method of  claim 14  wherein the organizational identifiers comprise one or more condition identifiers, each condition identifier able to identify MS data obtained from MS experiments having the same experimental conditions. 
     
     
         19 . The method of  claim 14  wherein the organizational identifiers comprise one or more replicate identifiers, each replicate identifier able to identify MS data obtained from a single replicate MS experiment. 
     
     
         20 . A system for generating and presenting mass spectrometry (MS) data to one or more users, said system comprising:
 a) an electronic host database able to store and MS data; and   b) a host processor programmed for processing and displaying MS data to the one or more users across a network, said host processor in communication with said host database and programmed to:
 i) receive one or more electronic peak tables comprising MS data from at least one of the one or more users; 
 ii) assign unique numerical identifiers to one or more subsets of said MS data in the one or more electronic peak tables based on input from the user submitting the electronic peak table, wherein the unique numerical identifiers identify data contained within the data subsets to be used in statistical analysis; 
 iii) store said data subsets with unique numerical identifiers in the host database; 
 iv) perform statistical analysis of said stored data subsets thereby generating analyzed MS data; 
 v) provide one or more data visualization options through the network to the one or more users, wherein said one or more visualization options correspond to one or more selectable graphs, charts, tables, or combinations thereof, able to display at least a portion of said analyzed MS data; 
 vi) independently receive one or more selected data visualization options from each of the one or more users; and 
 vii) independently generate and display one or more graphs, charts, tables, or combinations thereof, corresponding to the data visualization options selected by each of the one or more users, wherein the one or more graphs, charts, tables, or combinations thereof, are generated from the analyzed MS data. 
   
     
     
         21 . The system of  claim 20  wherein the one or more data visualization options and resulting one or more graphs, charts, tables, or combinations thereof, are provided through a web portal provided on the network connected to said host processor. 
     
     
         22 . The system of  claim 20  wherein said host processor is able to provide restricted access to an authorized portion of the one or more users, where the portion of the one or more users are able to view the web portal and download the analyzed MS data. 
     
     
         23 . The system of  claim 20  wherein said host processor is able to provide restricted access to an authorized portion of the one or more users, where the portion of the one or more users are able to submit electronic peak tables to the electronic database, select data visualization options to generate the graphs, charts, tables, or combinations thereof, and edit and/or remove said MS data. 
     
     
         24 . The system of  claim 20  wherein said host processor is able to provide restricted access to an authorized portion of the one or more users, where the portion of the one or more users are able to grant collaborating users access to the web portal and electronic database, and the ability to delete the web portal and electronic database entirely. 
     
     
         25 . The system of  claim 20  wherein said host processor is programmed to assign organizational identifiers to one or more subsets of said MS data in said one or more electronic peak tables based on input from the user submitting the electronic peak table. 
     
     
         26 . The system of  claim 25  wherein said processor is able to generate and display the MS data in an hierarchical manner, where the one or more graphs, charts, tables, or combinations thereof, are generated from analyzed MS data having the same organizational identifiers. 
     
     
         27 . The system of  claim 26  wherein the organizational identifiers comprise one or more identifiers selected from the group consisting of: project identifiers able to identify a unique MS project, branch identifiers able to identify a unique collection of protein, metabolite, or lipid MS data within a MS project, peak table set identifiers able to identify MS data obtained from the same electronic peak table, condition identifiers able to identify MS data obtained from MS experiments having the same experimental conditions, replicate identifiers able to identify MS data obtained from a single replicate MS experiment, and combinations thereof.