Proteomics Analysis Software | Shotgun Proteomics | DDA Proteomics

Software

SpectroMine ™

Unsurpassed Performance for DDA Proteomics.

Shotgun proteomics, also known as data-dependent acquisition (DDA), plays an important role in the generation of spectral libraries, qualitative proteome analysis, and the identification of post-translational modifications. In addition, recent innovations in isobaric labeling quantification, with the introduction of novel tags and wider multiplexing options, add accurate quantification of the proteome and widen the applications of shotgun proteomics for quantitative analysis.

      SpectroMine™ expands the possibilities for researchers in shotgun proteomics:

      • DIA, DDA and PRM Searchable: Increased versatility with the opportunity to search multiple data acquisition formats.
        Scalability to 1’000s of Runs: Memory-efficient data handling enables concurrent processing of >1’000 of MS runs.
        Accurate Statistics: FDR control on PSM, peptide, and protein level.
      • Differential Abundance Analysis: Detect previously undetectable information contrasting different biological or medical conditions.
        GO Support: Link your protein identifications to gene ontology annotations.
      • All-In-One Workflow: With integrated quality control, spectra, and post-analysis visualization.
        Isobaric Labeling Quantification: Compatible with Tandem Mass Tags (TMT), iTRAQ and EASI-tag reagents.
      Supported Instruments

       

      • Thermo Scientific™ Orbitrap Exploris™ 480
      • Thermo Scientific™ Q Exactive™ Series
      • Thermo Scientific™ Orbitrap Fusion™ Series
      • SCIEX TripleTOF® Series (5600, 5600+, 6600)
      • Bruker Impact II and timsTOF™ and timsTOF™ Pro
      • Waters Xevo® G2-XS QToF , Synapt G2-Si
      Supported Methods and Workflows

       

      • SpectroMine™ can search DDA, DIA, and PRM with MS1 information.
      • SpectroMine™ can search and quantify DDA runs from isobaric-labeled experiments using labels such as TMT, EASI-tag, and iTRAQ.
      • MS2 and SPS-MS3 methods are supported. All ion trap resolutions are supported. SpectroMine™ supports neutral loss-based fragmentation label methods (such as EASI-tag).
      Recommended System Requirements

       

      • Windows 10 x64
      • Intel or AMD CPU with 4 cores or more
      • 2 TB of hard drive space or more (2x data set size)
      • 16 GB of memory space or more

      If you are interested in ordering one of our softwares, please submit a request form or contact us. Our team will review your inquiry and get back to you within 5 working days.

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      Launch Pages
      SpectroMine™ 3: Unearth the Full Potential of DDA Proteomics

      SpectroMine 3 comes with many novel and enhanced features for unsurpassed performance for DDA proteomics.


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      Seminar Recordings
      Unearth the Full Potential of DDA Proteomics with SpectroMine™ 3

      Industry live seminar at the virtual annual HUPO conference 2021 featuring SpectroMine lead developer Tikira Temu and distinguished guest speaker Erwin M. Schoof.


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      Software Tutorials
      SpectroMine™ 3 Tutorial – How to analyze PTMs on fractionated TMT data

      Fabia Simona from Product Support walks you through the newest improvements to SpectroMine 3 related to the analysis of PTMs and fraction summarization in ILQ experiments.


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      Brochures & Flyers
      SpectroMine™ Brochure – Unsurpassed Performance for DDA Proteomics

      The brochure provides you with an overview of the key features and benefits which make SpectroMine the most powerful and user-friendly solution for DDA proteomics. The brochure ela [...]


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      Launch Pages
      SpectroMine™ 2: Unsurpassed Performance for DDA Proteomics

      The brochure provides you with an overview of the key features and benefits which make SpectroMine the most powerful and user-friendly solution for DDA proteomics.


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      Manuals
      SpectroMine™ Manual

      The SpectroMine manual is designed to support users and leverage their DDA and ILQ data analysis experience. It covers software features and analysis workflows and guides the user [...]


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      User Resources
      SpectroMine™ Demo Data Set

      contains: 10 raw files, FASTA file, Condition setup file, Experiment file (psar file), Source publication (Jan Muntel et al.)


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      Software Tutorials
      SpectroMine™ Tutorial – How to jump-start your data analysis

      Fabia Simona from our Product Support Team walks you through the analysis of Isobaric Labling Quantification (ILQ) data with SpectroMine. Get recommendations for important settings [...]


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      Software Tutorials
      Spectronaut™ Tutorial – How to visually inspect peptide-spectrum matches in Spectronaut™ & SpectroMine™

      Getting detailed information on peptide-spectrum matches (PSMs) is important to verify identifications and access to PSM information is required for data submission to many journal [...]


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      Seminar Recordings
      Raising Standards for DDA Data Analysis with SpectroMine™ – HUPO Connect 2020

      In this seminar held at HUPO Connect 2020, we launched SpectroMine 2, our software for DDA and isobaric labeling quantification (ILQ) workflows. The first part of the seminar cente [...]


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      Seminar Recordings
      Exploring Multiplexed Proteomics in Complex Applications with SpectroMine™ – HUPO Connect 2020

      In the context of HUPO Connect 2020 and the launch of SpectroMine 2, we invited two guest speakers to present their outstanding research. Dr. Mikhail Savitski and Prof. Erwin Schoo [...]


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