SpectroMine™ 2: Unsurpassed Performance for DDA Proteomics - Biognosys

SpectroMine™ 2: Unsurpassed Performance for DDA Proteomics

Launch Pages

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 elaborates on SpectroMine’s effortless isobaric labeling quantification, powerful search engine, and all-in-one workflow. Last but not least, ordering and customer support information is provided.

SpectroMine 2 is here and comes with several exciting new features and improvements.

Our powerful and user-friendly solution for DDA proteomics brings leading performance, speed, and support for the latest acquisition methods. SpectroMine integrates our state-of-the-art Pulsar search engine, offering full support for ion mobility technologies and achieving more identifications thanks to deep learning augmentation.

“SpectroMine is a game-changer for the analysis of multiplexed proteomics experiments. The speed and quality of analysis are unsurpassed.”

Dr. Mikhail Savitski,
EMBL Heidelberg

Key Features of SpectroMine


  • Unsurpassed Performance – The most powerful proteomics software for deep proteome coverage
  • Isobaric Labeling Quantification – User-friendly analysis pipeline for all isobaric labeling reagents, including TMTpro
  • Ion Mobility Support – Full support for different ion mobility-based acquisition platforms
  • Library-based Search – Better proteome coverage for challenging experimental setups
  • Search with Many Modifications – Fragment ion indexing for faster search with many different modifications
  • New Visualizations – New and improved ways to visualize your data
  • SpectroMine Viewer – Free software to browse annotated spectra and analysis results


SpectroMine 2 release notes

The Most Powerful Search Engine


SpectroMine brings the power of Pulsar, our industry-leading and vendor-independent database search engine, to DDA proteomics for deep proteome coverage and fast analysis.

Key Parameters of the
Benchmark Datasets

In total 9 datasets:

  • 8* were published 1, 2, 3, 4, 5-6, 7-8
  • Gradient lengths between 90 and 180 minutes
  • 7 ILQ datasets (TMT, TMTpro)
    • 2 datasets with MS2 quantification
    • 5 datasets withMS3 quantification
    • 10 – 24 fractions
  • 2 non-ILQ datasets
*Not published: reacquisition of dataset #8 with MS2 instead of MS3 quantification

With advanced deep learning models for indexed retention time (iRT) and fragmentation prediction, SpectroMine achieves unsurpassed proteome coverage.

We tested a range of software products using harmonized search space settings, protein inference, and False Discovery Rate (FDR) control. The results for datasets with and without isobaric labeling demonstrate that SpectroMine provides the most identifications and fastest processing times for a wide range of DDA experiments (see Figure).

SpectroMine lets you take full advantage of the latest instrumentation from all major vendors, including FAIMS Pro and PASEF ion mobility technologies, delivering state-of-the-art identification performance and short processing times.

At the same time, SpectroMine provides an intuitive interface to ensure data integrity and enables the sharing of data. FDR is rigorously controlled at peptide-spectrum match (PSM), peptide and protein levels, and a wide range of quality control visualizations are also available. To keep your results organized, they are saved in search archives, giving you full access to annotated raw data, and making it easy to share with anyone through the free SpectroMine Viewer.

Effortless Isobaric Labeling Quantification


SpectroMine provides a complete platform for isobaric labeling experiments. With integrated analysis templates for all major labeling reagents, staying on top of the latest innovations in the field is made easy.

DDA combined with isobaric labeling quantification (ILQ) is a discovery proteomics workflow, enabling quantification of multiple biological samples simultaneously in a single run (see upper Figure). ILQ delivers highly precise and reproducible quantification with deep proteome coverage [Muntel, 2019].

In just a few steps, ILQ analyses can be set up quickly and efficiently (see lower Figure). With automated calibration and smart default settings, optimal results can be achieved with minimal user input.

For experiments where the number of samples exceeds reporter multiplexity, samples can be organized in blocks/batches. SpectroMine offers experiment-wide normalization across these blocks. Moreover, workflows for assessing labeling efficiency allow you to quickly correct for sample preparation-related differences between analysis channels.

Quantification results can be viewed directly in SpectroMine, and then exported in either a customizable report format or with pre-packaged schemas for downstream processing with external tools such as MSstatsTMT.

SpectroMine can be configured for all Isobaric Labeling reagents and comes with presets for:

  • TMT (TMT (6-plex, 10-plex and 11-plex)
    TMTpro (16-plex)
    iTRAQ (4-plex and 8-plex)
    EASI-tag (6-plex)

Comprehensive Support for Ion Mobility based DDA


Take full advantage of the latest technologies in ion mobility based acquisition to improve proteome coverage. SpectroMine 2 supports PASEF (Bruker) and FAIMS Pro (Thermo Scientific) for DDA data, including ILQ experiments.

Over recent years, ion mobility has commercially emerged as an additional separation dimension for mass spectrometry data and has proven particularly useful to improve sensitivity in proteomics experiments.

SpectroMine offers a vendor-independent proteomics data analysis solution for the most recent ion mobility technologies.

PASEF Support:

SpectroMine can analyze PASEF data for both label-free and isobaric labeling quantification. It combines deep proteome coverage with impressively fast processing time, taking advantage of our Pulsar search engine’s optimization for PASEF data.

To benchmark SpectroMine performance, we used data from a published comparison of different DDA analysis tools [Yu, 2020]. In an example dataset with four replicate injections of HeLa samples, SpectroMine outperformed the results reported for other software by 10% or more in peptide identifications.

FAIMS Support:

DDA methods with FAIMS usually come in two main flavors: Single compensation voltage (CV) methods and multi-CV methods. Both of these methods are supported by SpectroMine for ILQ as well as label-free workflows.

In a recent publication [Schweppe, 2020], TMT10plex labeled mouse samples were enriched for phosphopeptides using the SL-TMT workflow [Navarette-Perea, 2018] and analyzed using a FAIMS Pro™ device.

Different multi-CV and no-CV setups were compared in order to test the influence of FAIMS on the number of quantifiable phosphopeptide identifications. We used SpectroMine to reanalyze the data acquired with a Thermo Fusion Lumos instrument (HCD fragmentation) and confirmed the benefit of using multi-CV FAIMS in these experiments.

Deeper Proteome Coverage with Library-based Search


Dig deeper into the proteome with library-based search of DDA data. Using a spectral library instead of a protein database for processing DDA data significally reduces the search space, resulting in improved sensitivity and greater analysis speed.

SpectroMine comes not only with powerful spectral library generation capabilities but also with the ability to search ILQ and label-free data using these libraries. This strategy can increase proteome coverage of DDA experiments [Lam, 2008] and is particularly useful when approaches such as pre-fractionation are not easily accessible. For example, this is the case in single-cell proteomics due to limited sample amounts.

As a proof of concept, we acquired a HeLa sample in 20 fractions and three replicate injections using DDA to create a spectral library (8360 Protein Groups). Three replicate injections (90 min gradient length) were searched once using a protein database and then once with the spectral library. The spectral library-based search led to approximately 18% more proteins being identified.

SpectroMine 2 is our latest DDA proteomics software and comes with many new features and state-of-the-art performance. Feel free to get in touch with us for a demo or trial license, and for help on upgrading your proteomics software to SpectroMine 2.

SpectroMine 2 Launch Webinar Series at HUPO Connect 2020



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