PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (2023)

PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (1)


PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (2)

High Throughput, All-in-One Software for Proteomics LC-MS/MS Analysis

High-Throughput, All-in-One Software for Proteomics LC-MS/MS Analysis

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Use PEAKS Online Xpro to take advantage ofpowerful,shared computing resources to perform LC-MS/MS protein and peptide identification and quantification analyses.With the ability to run on any all-in-one installation, multi-CPU/GPU cluster, or cloud server, the advanced software platform allows large datasets to be processed efficiently by multiple users at the same time.

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  • High Throughput, multi-user solution for large-scale projects and accelerated LC-MS/MS analyses
  • User friendly interface to create and save workflows, search parameters, and databases for routine analyses
  • True automation with PEAKS daemon: Automated Instrument Link and seamlessly connects your acquisition to your analysis in one easy to use workflow
  • Direct database search using DIA data with improved sensitivity and accuracy
  • Deep learning-based technology for predicting spectra, retention time, and collision cross-section values for Direct database search
  • Align your team’s efforts with administrative controls to standardise workflows, databases, PTMs, quantification methods, and project sharing
  • Vendor neutral including the latest MS technologies and compatible with all major MS vendors
  • GPU and clustered based solution that accelerates data analysis

PEAKS Online, means high-throughput proteomics data analysis for multiple users on a network. Although the term ‘Online’ is often associated with the world wide web, PEAKS Online should not be confused with public access. Instead, PEAKS Online is a software package which includes a Server licence and Client licences and can be hosted on a public cloud such as AWS or Google Cloud or it can be deployed on a private network such as your own high-performance computing cluster. This cloud-based architecture allows PEAKS Online to be fully parallelised and scalable to your lab’s needs and is ideal for processing large-scale projects.

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Distributed System for High performance Computing

PEAKS Online Xpro uses the latest distributed computing technology to achieve high-throughput performance with established PEAKS workflows for multiple users on a network.The Master is at the centre of the system, it accepts computing request from a client or directly from the MS instrument using an automated system; PEAKS daemon: Automated Instrument Link. The Master will distribute all the computing workload to different workers, where the computation is performed.All the data which is necessary for computation will be stored in the distributed database system.Since both computation and data storage are distributed to many different nodes,single node failure will not block the whole system. Therefore, the system is always accessible to the users.Additionally, because of the distribution,the system is also highly scalable, with the ability to add additional nodes at anytime to achieve maximum performance.

PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (3)

Streamlined Workflow with Direct Database search for DIA

DIA analysis is an appealing alternative to DDA workflows. In the past, DIA methods have relied on generating spectral libraries from DDA to identify and quantify peptides. PEAKS Online Xpro offers a unique DIA workflow to maximise identification of peptides by integrating three methods: spectral library search, direct database search, and de novo sequencing.

PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (4)
  1. A library search is performed against a pre-defined spectral library. Peptide spectra without a library match can be directly searched against a protein database.
  2. A protein sequence database is directly searched with DIA data. Advanced machine learning algorithms allow improved accuracy and sensitivity of peptide identification.
  3. Unmatched spectra from the database search are de novo sequenced.
  4. Identified peptides from both the spectrum library search and protein sequence database search can be used in a quantification analysis.

Note: All 3 search methods, PEAKS Spectral Library Search, Direct Database Search, and de novo sequencing are optional, and the steps of the workflow can be conducted independently or in sequence.

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PEAKS Workflow

PEAKS Online Xpro is designed to facilitate accurate and sensitive proteomic analysis using the PEAKS Xpro software workflows, but with higher performance on a shared resource. Users will be able to performde novo Sequencing,PEAKS DB Database Search,PEAKS Library Search, PEAKS PTM, andSPIDER, as in PEAKS Studio package. Optional PEAKS Q,andPEAKS IMS modules can be enabled, for labelled and label free protein quantification and ion mobility data support.

PEAKS Online provides users with the ability to utilise the established PEAKS workflows more efficiently and on a larger scale. The interactive tool used to send/retrieve data to/from the server is called PEAKS Client, and the results are presented in a similar manner as available in the PEAKS Studio desktop solution. Through the Web Client Interface or Client Command Line Interface (CLI), multiple users can also access the PEAKS Online server at the same time, supporting parallelism at the project and data level.

Smart data processing, is efficient data processing. If an analysis needs to be rerun with a new set of parameters, the whole workflow does not need to be reprocessed. This is perfect for certain applications like Time Course Studies and samples can be added to an existing project and workflows can be modified “on the fly”. PEAKS Online Xpro will only process the data that needs to be updated while keeping any of the relevant information generated previously. Once the desired results have been generated, users can export the results for each individualsample, or exportall the results at once in a single step.

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In PEAKS Online Xpro dual interfaces are available to ensure easy integration into any proteomics workflow. The Web Client Interface allows users to setup and submit projects visually, as well as review and validate their results. The Client CLI on the other hand can be integrated into existing pipelines to continue automated data processing.

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Web Client Interface

Access Administrative Tools
Setup, View and Share Projects
Monitor Ongoing Processes and Modify Priority
Accessible on any OS

Easily setup and access PEAKS projects from any computer, anywhere in the world. With PEAKS Online Xpro, users do not need to install any software files to access the server. Just open a web browser, like Google Chrome or Mozilla Firefox, to setup PEAKS searches and review the results. When your search task is done, the system will even send you an email to let you know the search is complete. Now you don’t need to worry about carrying your data around with you anymore!

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Client CLI

Automated Batch Data Processing
Define Standardised Workflows
Easily Integrate into Existing Pipelines
Reduce Manual Intervention

The command line interface gives users the ability to fully automate their data analysis. Simply establish standardised workflows so that once data is created in the repository, PEAKS Online Xpro will process and generate results instantaneously. Results generated using the Client CLI can be automatically exported into .csv files or viewed using the PEAKS Online Xpro Web Client.

PEAKS Online Xpro uses the latest technology of distributed computing to fully utilise the computing power of your hardware. The PEAKS Online Xpro architecture is built on the highly popular Apache Cassandra database system, which is used in heavy-load applications like Facebook and Netflix. PEAKS Online Xpro further distributes its computational workload to different workers using the Akka Actor system. This new setup gives PEAKS Online Xpro the ability to do a lot of things that is was not feasible in the PEAKS Studio desktop version. In particular, PEAKS Online Xpro is easily able to take on large-scale projects by more efficiently handling the increased workload of large cohort proteomics studies. In addition, its ready-to-scale, high-performance setup where the throughput and performance can be adjusted dynamically by changing the hardware configuration. Given the right resources, PEAKS Online Xpro can speed up data processing at least 10 times faster than PEAKS Studio and can handle 1000 samples or more.

In a recent benchmarking study, we compared the scalability of PEAKS Online Xpro as we increase the number of computing resources. The testing data set contained 56 samples where each sample was made up of 12 fractions. In total, we had 672 three-hour MS runs which composed of 5 million MS1 scans and 30 million MS2 scans. With the standard PEAKS Online Xpro 32-threads licence, it took about 10 days to finish the project, from data loading , data refinement, de novo sequencing, PEAKS DB, PEAKS PTM and SPIDER. However, when we increased the CPU cores, the performance increase linearly. With 512 cores, it took a little more than half day to finish the whole analysis.

PEAKS Online | Proteomics Server Software | Bioinformatics Solutions Inc. (24)

Summary of Dataset Used for Benchmark Analysis

# of Samples56
# of MS/MS Runs (180
# of MS5106521
# of MS/MS28858408
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PEAKS Online is distributed as a software package that includes a Server licence with multiple Client access. The base package of PEAKS Online includes 4 Client licences and can utilise up to 32 logical cores/threads. However, PEAKS Online is ready to scale, and researchers can increase the performance and/or number of users to meet the needs of any research group. The strength of the PEAKS Online Server and number of Client licences can be purchased to align the ideal solution.

# of Clients# of Cores/Threads

*Note: The number of cores/threads indicates the number of usable cores or threads that can be allocated to the PEAKS Online Server’s worker nodes.

Users can purchase additional individual client licences or a site client licence to meet their lab’s needs. For quantification and ion mobility data support, purchase the optional PEAKS Q and PEAKS IMS add-on respectively.

Overall, PEAKS Online Xpro is composed of 3 components: the Database Node(s), Master Node, and Worker Node(s). These can be distributed to different computers, or placed on the same machine. Each component has a unique pattern of computing resource usage and hardware requirements.

Database Node(s) of PEAKS Online Xpro store all application data and are the base for all proteomics processing. Since PEAKS Online Xpro is a distributed computing framework that can run from multiple machines, we use the popular distributed database system Cassandra as the main data storage to provide I/O performance at scale. Each data node, as part of a Cassandra cluster, has high demand for memory space and disk I/O speed.

The Master Node is the central hub of PEAKS Online Xpro’s computing framework. It takes charge of scheduling, dispatching, and synchronisation of computing tasks. Although it does not perform any data processing, it takes care of the web based user interface, loading of raw data and exporting of result data, and would benefit more from high performance CPUs.

Worker Nodes are responsible for the actual data processing and computation. PEAKS Online Xpro is easily scalable, so a worker node can be configured to use a customised number of CPU threads. As a rule of thumb, a worker node needs 2GB available memory for each computing thread and another 2GB spare memory for its own usage. Other than a few GB for logging, a worker node generally has no requirement for hard disk I/O speed nor space.

32 Thread Licence64 Thread Licence128 Thread Licence
Master6 Threads, 26 GB Memory8 Threads, 16 GB Memory16 Threads, 32 GB Memory
Cassandra8 Threads Each, 16 GB Memory Each, SSD (5T+)8 Threads Each, 16 GB Memory Each, SSD (5T+)8 Threads Each, 16 GB Memory Each, SSD (5T+)
Workers(16x): 32 Threads Total (4 Threads Per), 80 GB Memory (10 GB Per)

GPU Worker: 8 threads, 8G GPU memory, 32G system memory.

(16x): 64 Threads Total (4 Threads Per), 160 GB Memory (10 GB Per) GPU Worker: 8 threads, 8G GPU memory, 32G system memory.(16x): 128 Threads Total (8 Threads Per), 320 GB Memory (20 GB Per) GPU Worker: 8 threads, 24G GPU memory, 32G system memory.
All-in-one Installation:

INTELXEONGOLD 5120 Processor X2
(56 Threads including hyper threading)
Memory: 144GB
SSD: 500G (for OS)
SSD: 5T (for Cassandra) GPU: Nvidia GTX 1080 orNvidia Quadro P5000 16GB

All-in-one Installation:

INTELXEONGOLD6238 Processor X2
(88 Threads including hyper threading)
Memory: 256 GB
SSD: 500G (for OS)
SSD: 5T (for Cassandra) GPU: Nvidia GTX 1080 or Nvidia Quadro P5000 16GB

Cluster with 2 machines, each has the following hardware:

INTELXEONGOLD6238 Processor X2
(88 Threads including hyper threading)
Memory: 256 GB
SSD: 500G (for OS)
SSD: 5T (for Cassandra) GPU: Nvidia RTX 3090 or Nvidia Quadro RTX A6000

Note: Although PEAKS Online Xpro is best used in a cluster setting with dozens to hundreds of nodes, if you only have limited computing resources, one powerful workstation/server, you can still use it in standalone mode. In fact, all components of PEAKS Online can be started from the same machine. But in this case, you must make sure you have enough computing resources to accommodate the needs from all components.Cassandra has very intense usage of the hard drive. If everything is installed on the same machine, it’s highly recommended to have a separate high speed hard drive specifically for the data component.

References & Resources

PEAKS Online Xpro Brochure


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