Bringing Innovation to Shotgun 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. Recent innovations in isobaric labeling quantification, with the introduction of novel tags and wider multiplexing options, added accurate quantification of the proteome and widened 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 peptide and protein level
  • Differential Abundance Analysis: Detect previously undetectable information contrasting different biological or medical conditions.
  • GO Support: Link your protein identifications to genetic pathways


Faster Analysis.
Deeper Coverage.
Accurate Quantification.

SpectroMine™, the evolutionary proteomics software for data-dependent acquisition, is powered by Pulsar, Biognosys’ proprietary search engine. Pulsar’s main focus is spectral library generation. Given the challenge that spectral libraries are increasing in size, Pulsar has been designed to be fast and scalable, with up to thousands of mass spectrometry runs. SpectroMine expands on Pulsar’s core capabilities and is compatible with all three currently available isobaric labeling agents.








At its core, SpectroMine™ uses Biognosys’ proprietary search engine Pulsar, which is suitable to search raw files. In combination with the use of heuristic data computation, SpectroMine enables fast analysis times.






Increasing the number of identified peptides and proteins remains the key interest of scientists. SpectroMine™ calculates false discovery rates (FDR) on peptide- and protein levels and delivers accurate protein identifications.





SpectroMine™ has been designed to offer the highest usability in isobaric labeling quantification (ILQ) workflows and supports all current isobaric labeling quantification tags. SpectroMine is specifically able to leverage the increased accuracy that EASI-tags offer over alternative ILQ agents. SpectroMine is capable of accurately and precisely quantifying the MS2 reporter intensities of not only different proteins but also, individual PSMs. The obtained values closely matched the mixing ratios without signs of ratio compression, even in a two-proteome experiment.




Learn more about SpectroMine™

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