Cloud-Based Technologies for Mass Spectrometry

Connecting your laboratory to drive more insights from your data

Cloud-based technologies, including mass spectrometry analysis software, are becoming more prevalent in laboratories. These technologies can connect pieces of hardware, access the latest information to aid in processing large and complex datasets and obtain deeper insights into our data, both faster and with more confidence than ever before.

Discover how these technologies can facilitate instrument management to optimize utilization, allow remote access to check data acquisition, streamline problem solving and increase system uptime through instrument diagnostic sharing with Thermo Fisher Scientific service and support.

When it comes to making the most of your data, having access to the most up-to-date information ensures that you can dig deeper into your data and reveal new information, realizing the true value of your data and the actionable insights it contains. You can do all of this for free with a Connect account.

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mzCloud advanced mass spectral database

Small molecule identification is challenging, especially for many applications where reference standards are not available or easily accessed. Comprehensive mass spectral fragmentation libraries can provide the necessary confidence to identify compounds through a spectral match, fragment ion match, isotopic patterns or even ratios of fragment ions.

Covering a wide range of small molecule applications, the extensive structural and chemical diversity of mzCloud, ensures absolute confidence in any unknown identifications.

Making use of exhaustive high-resolution MS/MS and multi-stage MSn spectra, combined with extensive metadata, mzCloud offers the world’s largest (in terms of total spectra and data per compound) and most extensively curated mass spectral library and delivers powerful unknown identification capabilities.

Each mass spectrum has been filtered, recalibrated, averaged and fully structurally annotated. In addition to this high-quality data, each MSn fragmentation spectra have been acquired at various collision energies, for multiple adducts, with collision induced and higher energy collisional dissociation. The power of mzCloud comes alive when combined with mzLogic.

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Key benefits of mzCloud mass spectral database

Confidence for unknown identification Know more unknowns From spectra to structure Flexibility for research and routine applications
Comprehensive curation of all library content, with extensive, fully annotated and searchable fragmentation spectra, provides confidence in your results. Identify unknowns with automated deconvolution and library searching against extensive fragmentation spectra covering a wide chemical space, including small molecule applications With solutions to cover infusion or LC-MS, nominal or high-resolution data, you can be sure that your MSn spectra will provide you with actionable results, even when there is no spectral library match Access mzCloud directly through the Thermo Scientific Compound Discoverer or Thermo Scientific Mass Frontier software. Not online? mzVault provides you with the ability to perform off-line spectral library searching
Identify more unknowns with MSn and SubTree search

More unknowns can be confidently identified with MSn and substructure spectral matching, utilizing the full power of structure retrieval from online databases or user provided structures.

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Almanac mass spectrometry cloud-based monitoring

Monitor your LC-MS and GC-MS remotely from your desktop or mobile phone to increase your productivity and allow you to focus on other activities. Being able to see what is happening in real time, or receive e-mail and text notifications when your run is complete or an error occurs, means that you don’t have to worry about that all-important analysis.

Additionally, documenting system maintenance and other relevant information within the instrument logbook allows quick understanding of important recent activities such as calibration events for your laboratory analysts, who can also use Almanac to schedule instrument access time, maximizing system utilization.

Should something go wrong with your instrument, then "push to service" bundles all pertinent device-specific documents required by support teams to more efficiently address reported concerns (without sending any raw data, sample or personal information), reducing the time taken to accurately diagnose the issue and maximizing instrument uptime.

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Key benefits of Almanac mass spectrometry cloud-based monitoring

Keep your laboratory moving, even when you are on the go Understand your system’s history and what is happening in real-time Maximize instrument uptime
A busy laboratory does not have to be a challenge and should not require you to be present all of the time. Almanac enables users to schedule instrument access, view what is currently being acquired, and set up real-time notifications when sample sets have finished acquisition or if there is an error. Take control of your laboratory and data analysis, no matter where you are in the world. Being able to check when your instrument was last calibrated or serviced, or if your colleagues have left you an all-important notice doesn’t have to rely on a lab book, or a scrap of paper.

The instrument logbook records common user events and automatically enters them, allows service annotations and analysts to enter free text, add images and documentations so there doesn’t need to be any ambiguity as to the activity on the system.
When something doesn’t seem right, or there is a system error, it can be difficult to diagnose yourself or to obtain all of the relevant information for support teams to accurately diagnose the issue.

Now you have the option to share relevant instrument parameters and settings with our support teams when you place a call without sending any of your raw data or sample/personal information. This information better equips our service personnel to diagnose potential issues, and reduces the amount of time that your system may be unavailable.
Easily view your instruments' current status

Easily view your instruments’ current status using a mobile phone or desktop computer to check batch progress and remaining time to complete. Set up e-mail alerts to notify you of batch completion or if something goes wrong.

Cloud Connect Utility for data uploads

Manage and automate the secure upload of your data from your laptop or non-Almanac enabled PC into Connect using the Cloud Connect Utility. Uploading your data allows you to create a long term profile of your samples through Thermo Scientific Sample Profiler, discover over- or under-representation of proteins with Thermo Scientific Pathway Over-representation, or utilize Venn diagrams to compare and visualize protein memberships using the Omics Comparator application.

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Key benefits of the Cloud Connect Utility

Secure and share your data Obtain more insights with Connect tools
With the Cloud Connect Utility, you can securely upload your data files to your Connect account, either manually or automatically. This data can be stored, or you can use it to back up your files, safeguarding against any potential loss should something happen to your desktop computer. When you can see the real-time upload status of your data, you instantly know where it is and can securely share it with your colleagues or utilize the web-based applications within Connect to further interrogate your data. Once your data is safely stored within your Connect account, you can easily interrogate it further using the web-based applications within Connect. Sample Profiler allows you to perform differential comparison of your samples, long term trending and compound profile analysis with powerful data visualization; Pathway Over-representation digs deeper into your data to detect proteins that are over-/under-represented and the pathways to which they correspond; for omics and gene data, Omics Comparator visualizes common and unique proteins from multiple lists, and you can drill down to understand more about molecular, cellular and biological function.
Sample Profiler profile comparison tool

Profiling samples long term can reveal insights that are not immediately obvious. For example, Sample Profiler allows you to reveal more about your data by comparing profiles between batches, or trends in sampling locations over time.

Whether you are analyzing samples for environmental monitoring, metabolomics, food authenticity, forensic toxicology, extractables and leachables, or any other purpose, isn’t it time to take a deeper look?

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Key benefits of the Sample Profiler tool

Create multiple profiles to compare more See what’s the same, and what’s different Visualize your data and identify markers to follow
Once your data are uploaded into your Connect account, you can maximize the information you obtain by creating multiple profiles that relate to your study factors, experimental design or other criteria you wish to use to characterize your samples. With multiple profiles or sample types, you can easily perform comparisons, revealing different fold changes and see statistical analysis through p-values, all graphically displayed to make it simple to observe trends and see what is normal, or what has changed significantly. Discover more, faster. Use trend line plots, observe differences in concentrations of given compounds when visualizing trends in your data, or search for the presence or absence of marker compounds using compound name, formula, molecular weight or retention time.
Visualize the data across your samples

Create profiles and view by compound or see comparisons and follow market compounds across large datasets, with multiple options for how to visualize the data across your samples.

Trendlines show variation in compound intensities across samples/time

Trendlines show variation in compound intensities across samples/time, with data tables showing related statistical information about ratios between profiles, p-values, fold changes and distribution across samples.

Pathway Overrepresentation pathway analysis tool

After using Proteome Discoverer for quantitative proteomics analyses, use the Thermo Scientific Pathway Over-representation application to make sense of proteins and pathways that are over- and underrepresented in your sample.

Take any of your protein or gene lists and enter them into the web-based Pathway Over-representation app to detect biological pathways that are either over- or under-represented. Significant WikiPathways, Reactome and, optionally, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are reported, with a range of visualization and interactivity tools to better understand the pathways that exhibit over/underrepresentation.

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Key benefits of the Pathway Over-representation tool

Find significant pathways from your protein or gene lists View gene ontology and other annotation details
Once you have determined significant differentiators from your study by using the Thermo Scientific Proteome Discoverer software, for example you can make sense of the resulting protein list by determining over-represented pathways based on Reactome, WikiPathways or KEGG annotations. From the significant pathways, the statistical significance can be observed, as well as the underlying proteins/genes that form these pathways. More information about the proteins (or genes) is easily accessed, with detailed annotation information and links to further information available. Data can be visualized in histograms, or chiclets plots to better understand the roles of identified proteins or genes.
Simple graphical representation of over- and under-represented proteins and genes

Simple graphical representation of over- and under-represented pathways from protein or gene lists provides an overview of the statistical significance and is interactive to allow you to drill down and observe more information about the pathways and proteins/genes which are over-/under-represented.

Proteins in pathway histogram

When drilling down to the proteins in a given pathway, you can choose between histogram and chiclet plots to visualize between the number of proteins and their molecular function, cellular function and biological processes in which they are involved, with further information for each protein being easy to access.

Omics Comparator comparison tool

Take any of your protein or gene lists and enter them into the web-based Thermo Scientific Omics Comparator application to quickly and easily observe what is shared or unique between two or up to five different protein or gene lists at any one time. Drill down into any area to view detailed information and links to further information about the proteins/genes involved.

It could be that you are looking to compare experimental improvements, and easily see what improvements you have made to your workflow regarding additional identifications. Compare your proteins and genes and see more of what you’ve been missing.

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Key benefits of the Omics Comparator application

Quickly see overlap and uniqueness between protein or gene lists Dig deeper into the commonalities, or uniqueness
Omics Comparator provides the versatility required for you to make informed decisions. For example, you might make biological comparisons across multiple samples under different stress conditions, or improve a Proteome Discoverer workflow with a single dataset.

Resulting Venn diagrams facilitate rapid data interrogation. For example, comparing different search parameters for a single data file, or for genes, set memberships appear together with annotations, including color-coded Gene Ontology (GO) terms for individual molecular entries in each set.
Using the resulting Venn diagrams, quickly drill down into the proteins or genes that are shared or unique across the data lists being compared.

As with the Pathway Over-representation app (whose inputs can also be used in Omics Comparator), the proteins and genes can be listed with access to further information or data visualization as chiclets or histograms to understand the molecular, cellular and biological functions and processes.
Venn diagram comparing five lists of proteins from E. coli samples being subjected to stress

Venn diagram comparing five lists of proteins from E. coli samples being subjected to stress. From the diagram, the shared or unique proteins can be accessed with further information and data visualization tools available to better understand the data relationships.

Proteins in Set histogram

Histogram plotting for the molecular functions of the proteins that were unique to the stressed E. coli sample 1. Further views of cellular function and biological processes are available, with chiclet views allowing accession information for each protein or gene.

Connect your lab to drive more insights from your data

Connect your lab to drive more insights from your data

Small molecule characterization and identification clouding your decision making? Cloud-based technologies, including mass spectrometry analysis software, are becoming more prevalent in laboratories.

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