Web-based data upload and visualization platform enabling creation of code-free exploration of MS-based omics data

Patent metadata

Field	Value
Publication number	US-12373084-B2
Application number	US-202117360806-A
Country	US
Kind code	B2
Filing date	Jun 28, 2021
Priority date	Jul 31, 2017
Publication date	Jul 29, 2025
Grant date	Jul 29, 2025

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.

First claim

The invention claimed is:

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) performing a plurality of MS experiments, wherein performing each MS experiment comprises generating fragment ions from a sample comprising a protein, metabolite, or lipid, measuring a fragmentation spectrum for the sample, wherein the fragmentation spectrum comprises a plurality of peaks corresponding to measured mass-to-charge ratios of the fragment ions from the sample, and generating multiple electronic peak tables comprising MS data,
wherein the plurality of MS experiments comprises analyzing samples from at least two groups selected from the group of protein samples, metabolite samples, and lipid samples;
c) performing at least one replicate MS experiment having experimental conditions that are the same as at least one of the plurality of MS experiments, wherein performing each replicate MS experiment comprises generating fragment ions from a second sample comprising a protein, metabolite, or lipid that is the same as at least one of the plurality of MS experiments. measuring a fragmentation spectrum for the second sample, wherein the fragmentation spectrum comprises a plurality of peaks corresponding to measured mass-to-charge ratios of the fragment ions from the second sample, and generating additional multiple electronic peak tables comprising MS data;
d) assigning unique numerical identifiers to one or more subsets of said MS data in said electronic peak tables from the plurality of MS experiments and the at least one replicate MS experiment, wherein the unique numerical identifiers identify data contained within the data subsets to be used in statistical analysis;
e) assigning organizational identifiers to said one or more data subsets, wherein the organizational identifiers comprise:
i) one or more project identifiers, each project identifier able to identify a unique MS project;
ii) 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;
iii) one or more peak table set identifiers, each peak table set identifier able to identify MS data obtained from the same electronic peak table;
iv) one or more condition identifiers, each condition identifier able to identify MS data obtained from MS experiments having a same specified experimental condition; and
v) one or more replicate identifiers, each replicate identifier able to identify MS data obtained from a single replicate MS experiment relating to a specific molecule, wherein MS data obtained from a single replicate MS experiment is also assigned one or more condition identifiers;

f) storing said data subsets with organizational identifiers and unique numerical identifiers in said electronic database;
g) determining average molecule abundance from the electronic peak tables of specific molecules present in the replicate MS experiments having the same specified experimental condition from said stored data subsets and performing statistical analysis of said stored data subsets thereby generating analyzed MS data containing quantitative data of said specific molecules;
h) 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;
i) receiving one or more selected data visualization options from the user;
j) 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 analyzed MS data, wherein analyzed data relating to said specific molecules is searchable using organizational identifiers selected by the user; and
k) 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.

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 restricted access, wherein said restricted access allows an authorized user to view the web portal and download the analyzed MS data.

8. The method of claim 7 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.

9. The method of claim 7 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.

Assignees

• Wisconsin Alumni Res Found

Inventors

• Kwiecien Nicholas William
• Westphall Michael Scott
• Coon Joshua Jacques

Classifications

• G06T11/26

  Drawing of charts or graphs · CPC title

• H04L63/104

  Grouping of entities · CPC title

• G06Q10/10

  Office automation; Time management · CPC title

• G06Q10/101

  Collaborative creation, e.g. joint development of products or services · CPC title

• G06F16/958

  Organisation or management of web site content, e.g. publishing, maintaining pages or automatic linking · CPC title