OneOmics suite

Cloud-based mass spectrometry software

“Drive big data to meaningful insights with cloud computing”

Use the power of cloud-based software at your fingertips to extract and visualize mass spectrometry-generated big data from proteomics, metabolomics and genomics projects on a single platform. Turn that data into biological insights quickly, and share your results widely and easily with collaborators.

Contact SCIEX to request more information or a demo of this software.

Data Store and Experiments

Organize and create

In these workspaces, you can assemble and define the metadata in your study.

Build experiments from uploaded data
Share projects, such as data and results
Assign study-level metadata
Build experiments and add them to studies
- Proteomics SWATH DIA data
- Metabolomics SWATH DIA data
- RNA expression data
- Protein identification data
- iTRAQ reagent protein expression data
- Templates available for metadata assignments

Access and manage data uploaded to the cloud with SCIEX
Store your processed results files
Share files with collaborators

ProteinPilot

Identify and quantify proteins faster

Identify

This workspace enables you to process data dependent acquisition (DDA) data. Database searches can be performed using the Paragon and Pro Group algorithms. Perform protein identification and build out your ion library.

Identify proteins

Process a "multi-file" search
Process a "per-file" search

View your results

View database search result metrics
View protein identification results
View MS/MS data with matching ions

Assess underlying data quality with analytics

View the number of proteins and peptides identified at critical false discovery rate (FDR) values
Assess the quality of your chromatography and digestions
Dive into each panel to discover more detailed information
View proteins identified and sorted according to their unused protein score

Ion Library

Create spectral ion libraries from DDA

Identify

This workspace enables you to process data dependent acquisition (DDA) data. The protein identifications are leveraged to help you build out your ion library.

Identify proteins
- Process a "multi-file" search
- Process a "per-file" search
Navigate to your ion libraries using shortcuts
Ion libraries are made for use in the Proteomics workspace of OneOmics suite, and they can also be used as is for DIA-NN workflows

Proteomics

Quantified and visualized

This workspace contains several applications to help further your research and the processing of your SWATH acquisition data.

Extractor application functions include:

Merges and retention time (RT) aligns selected ion libraries
Performs RT calibration on each SWATH acquisition file
Extracts and integrates the fragment ion extracted ion chromatogram (XIC) area using the final ion library
Peptide peak group scoring for false discovery rate (FDR) analysis

Assembler application functions include:

Normalization which adjusts the peak area tables to be on the same scale for all experiments
Fold change analysis to determine direction, extent and confidence of peptide and protein fold changes

Analytics dashboard

Visualize your mass spectrometry proteomics data quality.

Reproducibility
FDR analysis
Retention time calibration
Dynamic range

Browser dashboard

Visualize protein expression results in a clear and concise format.

Sample grouping
Normalization quality
Ontologies
Protein fold changes
- Box and whisker plots
- Peptide fold change across protein sequences

Protein heat map

The protein heat map functionality delivers an overview of the protein expression results. This user-friendly format allows the operator to adjust filters to refine the heat map. With the vast data capture you can drill into a single protein to see changes across samples throughout the sequence.

DIA Results

Quantified and visualized

Quantify

This workspace contains several applications to help further your research and the processing of your SWATH DIA data. The powerful visuals for SWATH offered in the Proteomics workspace are now available for DIA-NN results.

Transform application

Translates a DIA-NN multi-sample main result to a sample-specific result that is compatible with OneOmics suite

Assembler application

Normalization that adjusts the peak area tables to be on the same scale for all experiments
Fold change analysis to determine the direction and extent of peptide and protein fold changes with confidence

Metabolomics

Quantified and visualized

In this workspace, you can extract key metabolite areas from your acquired data and then normalize and compute fold changes (FCs) and confidences. You can also assess the MS data quality and visualize changes across a study.

Within this workspace the Extractor extracts and integrates compound peaks using NIST20 and the Accurate Mass Metabolite Spectral Library (AMMSL).

Another feature is the Assembler functionality, which adjusts the peak area tables to be on the scale for all experiments.

Fold change (FC) analysis is also supported in this workspace to determine the direction, extent and confidence of metabolite FC.

Analytics dashboard

Visualize your mass spectrometry metabolomics data quality.

Reproducibility
FDR analysis
Dynamic range

Browser dashboard

Visualize metabolite expression results in a clear and concise format.

Sample grouping
Normalization quality
Ontologies
Metabolite fold changes
- Box and whisker plot
- Metabolite and transition peak areas across samples

Metabolite changes heat map

The metabolite heat map delivers an overview of the metabolite changes within your study allowing you to adjust filters to refine the plot. The comprehensive data captured and processing allows you to drill into single analytes to see changes across samples throughout the sequence.

iTRAQ

Labeled quantification

This workspace enables you to interrogate quantitative data obtained from samples labeled with the multiplexed, amine-specific, stable isotope iTRAQ reagent kits:

Identify proteins and process either a “per-file” or a “multi-file” search
Quantify using iTRAQ reagents
- Bias correction
- Normalization
- Background correction
Build a workspace
- View database search result metrics
- View protein identification results
- View MS/MS data with matching ions
- Download group files and view in the ProteinPilot workspace

Replenish your iTRAQ reagents stock here

BioReviews

Integrate multi-omics studies

Compare and assess different omics studies. Within BioReviews you can compare quantitative data between genomics, proteomics and metabolomics experiments.

It includes functionality for aligning genomics and proteomics results, or comparing multiple proteomics or multiple metabolomics data sets.

Combine studies to align your big data
Perform cluster analysis and trend analysis to find key similarities and differences in protein, metabolite or RNA quantitative data
Determine the biological significance of your similarities and differences
View enriched biological pathways

Another feature in this workspace is support for manual conflict resolution when a protein maps to multiple genes or a single gene maps to multiple proteins.

You can also perform multiple analyses on experiment sets, which are each shown as a tile, and view the settings used and links to the results:

Intersection: shows overlap between every PCA-PCVG and K-means group
K-means: shows the clusters found
PCA-PCVG: shows the trends found
PCA-DA PCA: considering known sample grouping
T-test: displays a plot of log2 fold change versus the confidence or -log10(p-value), for every contrast
Area and fold change analysis

Cloud-based mass spectrometry

Fast, secure and shareable

The advancements in cloud-based software are enabling researchers to interrogate big data faster than ever before. The cloud computing integrated into the OneOmics suite can distill multi-omics data from transcriptomics and mass spectrometry data all in one place

Analyze faster

Avoid queues and backlogs of samples waiting to be processed, and get secure, precise information at revolutionary speeds.

Up to 10x faster than desktop processing
Process many analyses all at once without losses in performance
User-friendly app environment for large-scale data processing
Integrated tools to create workflows within a single environment

Securely store and manage

Process your data with confidence and assured of the highest security protocols. Manage your studies with ease and organize your results to reflect your lab's configuration.

Amazon Web Services (AWS) security standards, multi-site synchronous storage
Securely send data from the instrument to the cloud environment
Reduces the need for on-site storage and computing power

Share and collaborate

Partnerships can flourish synchronously through OneOmics suite, as its power and fidelity makes communicating and processing data on shared timelines easy. Any party involved can simply log in and get started.

Easily share projects (data and results)
No more FTP sites or shipping hard drives
Access data and results, from anywhere and at anytime

One cloud. Countless opportunities.

Productivity gains

Process more samples and get more results! Our cloud-based mass spectrometry data processing can significantly expand your lab’s productivity by running high volumes of data analysis at the same time.

Powerful visuals

Visualize your data in different ways by exploring all omics approaches simultaneously, giving your research and your funding proposals an edge.

Scalability

With OneOmics suite, you can process data of any size, at any time and from any place, without the need to own the infrastructure. By working in the cloud, your projects won't be limited.

Speed

Cloud-based processing can run and distill data from multiple sources all at once. Avoid queues and backlogs of samples waiting to be processed, and get secure, precise information at revolutionary speeds.

Quick installation

Cloud-based software is installed with ease. Expect no additional time or financial requirements and no trouble with data processing and storage. Look forward to simple monthly payments followed by remote updates

OneOmics suite subscriptions

Choose a subscription that best suits your lab's analysis and research.

Proteomics

Base subscription for proteomics applications:

IDA data processing using ProteinPilot app for protein identification and ion library creation
SWATH acquisition data processing for relative quantification
Results visualization: fold change heat maps, volcano plots, gene ontology plots, etc.
Pathway analysis using the UniProt knowledge base and reactome.org pathway database
Tools for transforming, assembling and visualizing your DIA-NN reports

Includes:

Data store account with 4 TB space for data and results
- Approximately 1,000 samples at 4 GB each
- Tools for transforming, assembling and visualizing your DIA-NN reports
Processing time allocation for approximately 1,000 samples
Technical support via phone, email and website

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Metabolomics

Base subscription for metabolomics applications:

NIST20 and Accurate Mass Metabolite Spectral Library (AMMSL) SWATH acquisition data processing for relative quantification
SWATH acquisition data processing for relative quantification
Results visualization: fold change heat maps, volcano plots, etc.
Pathway analysis using the Human Metabolome Database (HMDB) and reactome.org pathway database

Includes:

Data store account with 3 TB space for data and results
- Approximately 3,000 samples at 1 GB each
Processing time allocation for approximately 3,000 samples
Technical support via phone, email and website

Buy now

Multi-omics

Base subscription for multi-omics applications:

IDA data processing using ProteinPilot app for protein identification and ion library creation
NIST20 and Accurate Mass Metabolite Spectral Library (AMMSL) for metabolomics
SWATH acquisition data processing for relative quantification
Results visualization: fold change, volcano plots, and many more plots
Pathway analysis using the UniProt knowledge base, HMDB and reactome.org pathway database
Tools for transforming, assembling and visualizing your DIA-NN reports

Includes:

Data store account with 6 TB space for data and results:
- Approximately 1,000 proteomics samples at 4 GB each plus
- Approximately 2,000 metabolomics samples at 1 GB each (or equivalent combination)
Processing time allocation for approximately 1,000 proteomics samples and 2,000 metabolomics samples (or an equivalent combination)
Technical support via phone, email and website

Buy now

Compatibility

The SCIEX portfolio of QTOF systems delivers unmatched speed, robustness and accuracy for the assays you need to run today and tomorrow.

ZenoTOF 7600 system

This accurate mass spectrometer gives richer, more comprehensive data with powerful innovations for Omics research. EAD fragmentation and Zeno trap technology pave the way to obtain sensitive and informative MS/MS data.

Learn more

TripleTOF 6600+ system

This high-performance accurate mass spec solution offers a combination of qualitative and quantitative analysis and advanced workflow capabilities. Optimized for large-scale quantitative mass spectrometry, the TripleTOF 6600+ system offers sensitive and robust performance

Learn more

Application notes and useful information

SCIEX community

Join the discussion

Take the time to create a SCIEX account and join the various communities that are available. These communities are a platform for interacting with your peers around the globe to share and exchange ideas and expand your research. You can also stay up to date on new innovations in software, mass spectrometry, capillary electrophoresis and other SCIEX products