OneOmics

OneOmics suite is a cloud-based mass spectrometry software platform developed by SCIEX for processing and visualizing multi-omics data from proteomics, metabolomics, and genomics projects. It is designed for researchers conducting large-scale cohort studies who need to handle high volumes of data generated from SWATH acquisition, data-dependent acquisition (DDA), and DIA-NN workflows. The platform consolidates data extraction, quantification, visualization, and cross-omics comparison into a single cloud environment, enabling teams to share results with collaborators without relying on physical data transfer methods.

The suite is organized into distinct workspaces, each addressing a specific stage or data type in the multi-omics workflow. Processing runs on Amazon Web Services (AWS) infrastructure, which SCIEX states can deliver up to 10x faster analysis compared to desktop processing, while supporting concurrent analysis of multiple sample sets without performance degradation.

Data Store and Experiments

• Build experiments from uploaded data and assign study-level metadata
• Supports multiple data types: Proteomics SWATH DIA, Metabolomics SWATH DIA, RNA expression, protein identification, and iTRAQ reagent protein expression data
• Templates available for metadata assignments
• Share projects, including data and results, with collaborators
• Access and manage data uploaded to the cloud; store processed results files

ProteinPilot Workspace

• Processes data-dependent acquisition (DDA) data using the Paragon and Pro Group algorithms
• Supports both multi-file and per-file database searches for protein identification
• View database search result metrics, protein identification results, and MS/MS data with matching ions
• Analytics tools to assess data quality, including proteins and peptides identified at critical false discovery rate (FDR) values, chromatography and digestion quality, and proteins sorted by unused protein score

Ion Library Workspace

• Processes DDA data to build spectral ion libraries from protein identifications
• Supports multi-file and per-file searches
• Ion libraries created here are compatible with the Proteomics workspace within OneOmics suite and can also be used directly in DIA-NN workflows
• Shortcuts available to navigate to generated ion libraries

Proteomics Workspace

• Extractor application merges and retention time (RT) aligns selected ion libraries, performs RT calibration on each SWATH acquisition file, extracts and integrates fragment ion XIC areas, and performs peptide peak group scoring for FDR analysis
• Assembler application normalizes peak area tables across experiments and performs fold change analysis to determine direction, extent, and confidence of peptide and protein fold changes
• Analytics dashboard visualizes data quality metrics including reproducibility, FDR analysis, retention time calibration, and dynamic range
• Browser dashboard displays protein expression results with sample grouping, normalization quality, ontologies, protein fold changes shown as box and whisker plots, and peptide fold change across protein sequences
• Protein heat map provides an overview of protein expression results with adjustable filters; supports drilling into individual proteins to view changes across samples

DIA Results Workspace

• Extends SWATH proteomics visualization capabilities to DIA-NN results
• Transform application translates a DIA-NN multi-sample main result into a sample-specific result compatible with OneOmics suite
• Assembler application normalizes peak area tables and performs fold change analysis for peptide and protein fold changes with confidence metrics

Metabolomics Workspace

• Extractor extracts and integrates compound peaks using NIST20 and the Accurate Mass Metabolite Spectral Library (AMMSL)
• Assembler adjusts peak area tables to a common scale across experiments
• Fold change analysis determines direction, extent, and confidence of metabolite fold changes
• Analytics dashboard covers reproducibility, FDR analysis, and dynamic range
• Browser dashboard shows metabolite expression results with sample grouping, normalization quality, ontologies, metabolite fold changes as box and whisker plots, and metabolite and transition peak areas across samples
• Metabolite heat map provides an overview of metabolite changes with adjustable filters and the ability to drill into individual analytes

iTRAQ Workspace

• Supports quantitative data from samples labeled with multiplexed, amine-specific, stable isotope iTRAQ reagent kits
• Protein identification via per-file or multi-file searches
• Quantification using iTRAQ reagents with bias correction, normalization, and background correction
• View database search result metrics, protein identification results, and MS/MS data with matching ions
• Download group files for viewing in the ProteinPilot workspace

BioReviews Workspace

• Integrates and compares quantitative data across genomics, proteomics, and metabolomics experiments
• Supports alignment of genomics and proteomics results, and comparison of multiple proteomics or multiple metabolomics datasets
• Cluster analysis and trend analysis to identify similarities and differences in protein, metabolite, or RNA quantitative data
• Biological significance assessment and enriched biological pathway viewing
• Manual conflict resolution when a protein maps to multiple genes or a single gene maps to multiple proteins
• Multiple analysis types available per experiment set: Intersection, K-means clustering, PCA-PCVG trend analysis, PCA-DA, T-test (log2 fold change vs. confidence or -log10(p-value)), and area and fold change analysis

Cloud Infrastructure and Collaboration

• Processing is up to 10x faster than desktop processing, with the ability to run many analyses simultaneously without performance loss
• Secured using Amazon Web Services (AWS) standards with multi-site synchronous storage
• Data can be sent securely from the instrument directly to the cloud environment
• Reduces the need for on-site storage and local computing infrastructure
• Projects, data, and results can be shared with collaborators; access is available from any location at any time
• No FTP sites or physical hard drive transfers required

Subscription Tiers

• Proteomics subscription: Includes IDA data processing via ProteinPilot, SWATH acquisition processing, results visualization (fold change heat maps, volcano plots, gene ontology plots), pathway analysis using UniProt and reactome.org, DIA-NN report tools, 4 TB data storage (approximately 1,000 samples at 4 GB each), and processing allocation for approximately 1,000 samples
• Metabolomics subscription: Includes NIST20 and AMMSL SWATH acquisition processing, results visualization (fold change heat maps, volcano plots), pathway analysis using HMDB and reactome.org, 3 TB data storage (approximately 3,000 samples at 1 GB each), and processing allocation for approximately 3,000 samples
• Multi-omics subscription: Combines proteomics and metabolomics capabilities, including IDA processing, AMMSL metabolomics processing, SWATH quantification, results visualization, pathway analysis using UniProt, HMDB, and reactome.org, DIA-NN report tools, 6 TB data storage (approximately 1,000 proteomics samples plus approximately 2,000 metabolomics samples), and corresponding processing allocations
• All subscriptions include technical support via phone, email, and website

OneOmics suite is compatible with SCIEX QT