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Software

Spectronaut X™

Discovery proteomics software for the targeted analysis of DIA measurements from various MS platforms.

Enables maximal proteome coverage and data completeness by utilizing the power of Hybrid Libraries – combining core proteome libraries (project or resource libraries) with sample-specific libraries (directDIA).

Please take a look at our General Software License.

Spectronaut X™

Product number: Sw-3001

Data independent acquisition (DIA) has become the method of choice for discovery proteomics workflows. Spectronaut™ has been able to achieve the highest protein coverage and data completeness through its cutting-edge data analysis algorithms including integrated search engine Pulsar.
Spectronaut X™ offers novel workflows to significantly extend the number of research applications:

  • Hybrid Library Generation: By combining core proteome libraries (project or resource libraries) with sample-specific libraries (directDIA), the number of quantifiable proteins can be increased
  • Spike-in Workflow: In combination with Biognosys’ new PQ500 reference peptide kit, targeted proteins can be label-free quantified using a comprehensive reference calibration curve spanning five orders of concentration
  • Host-Cell Proteins: Calibration carry-over allows for higher precision in identification and quantification of low abundance host-cell proteins

Spectronaut X™ also includes new features that facilitate the data analysis through improved performance and visualization:

  • Extensive spectral libraries: Increased performance and memory efficiency allows processing of very large experiments
  • Data match plot: Filters to choose which matched ions to visualize
  • Protein-coverage plot: More classes of peptides annotated with streamlined run overview

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Supported Instruments

  • Thermo Scientific™ Q Exactive™ Series
  • Thermo Scientific™ Orbitrap Fusion™ Series
  • SCIEX TripleTOF® Series (5600, 5600+, 6600)
  • Bruker Impact II
  • Bruker timsTOF™ and timsTOF™ Pro (without ion mobility)
  • Waters Xevo® G2-XS

Supported Methods

Spectronaut X™ analyzes raw data from a large variety of different methods:

  • DIA
  • WiSIM-DIA
  • SWATH™
  • SWATH™ 2.0
  • SONAR™

Methods should acquire MS1 and MS2 or MS2 only scans. The cycle time of the method should be in the range of 1-3 seconds depending on your average peak width. Fractionation, including gas phase fractionation, is supported.

 

Minimum System Requirements

  • Windows 7 x64
  • Intel Core™ CPU 2.7 GHz (quad core) or similar
  • 500 GB of free HDD space
  • 16 GB of RAM memory
  • .NET Framework 4.7

 

Expected memory consumption

 

How to Order

Please submit a request form. Our team will review your inquiry and get back to you within 5 working days.

 

 

Please contact us for support.

Spectronaut X™ Manual

Spectronaut X™ Brochure

FASTA of iRT peptides for shotgun search

Skyline Schema for exporting Spectronaut compatible libraries - simply add this schema to Skyline's report list

 

Test Files

Spectral library generation using Proteome Discoverer 1.4 (HEK293 cell line sample)

Proteome Discoverer 1.4 Search Files (zip, 1.3 GB) for spectral library generation

 

Spectral library generation using MaxQuant 1.5 (HEK293 cell line sample)

MaxQuant Search Files (zip, 386 MB) for spectral library generation

 

HEK293 demo data set

Description Demo Data Set (pdf file)

HTRMS Spectronaut™ Sample 1 Run 1 (htrms file, 2.9 GB)

HTRMS Spectronaut™ Sample 1 Run 2 (htrms file, 3.4 GB)

HTRMS Spectronaut™ Sample 1 Run 3 (htrms file, 3.0 GB)

HTRMS Spectronaut™ Sample 5 Run 1 (htrms file, 3.4 GB)

HTRMS Spectronaut™ Sample 5 Run 2 (htrms file, 3.4 GB)

HTRMS Spectronaut™ Sample 5 Run 3 (htrms file, 2.9 GB)

HTRMS Spectronaut™ Sample 8 Run 1 (htrms file, 3.1 GB)

HTRMS Spectronaut™ Sample 8 Run 2 (htrms file, 3.3 GB)

HTRMS Spectronaut™ Sample 8 Run 3 (htrms file, 2.9 GB)

Spectral library HEK (kit file, 73MB)

 

HEK293 demo data set

SWATH™ Spectronaut HEK293 Demo R01 (wiff-file, 8.8 MB)
SWATH™ Spectronaut HEK293 Demo R01 (wiff-file.scan, 3.8 GB)

SWATH™ Spectronaut HEK293 Demo R02 (wiff-file, 8.8 MB)
SWATH™ Spectronaut HEK293 Demo R02 (wiff-file.scan, 3.8 GB)

SWATH™ Spectronaut HEK293 Demo R03 (wiff-file, 8.8 MB)
SWATH™ Spectronaut HEK293 Demo R03 (wiff-file.scan, 3.8 GB)

Spectral library HEK293 (tsv file, 34.0 MB)

 

HEK cell line sample

RAW Test Data Set 1 (raw file, 2.4 GB)

RAW Test Data Set 2 (raw file, 2.8 GB)

RAW Test Data Set 3 (raw file, 2.5 GB)

Spectral library HEK293 (xls file, 4.2 MB)

Spectral library E. Coli (xls file, 5.9 MB)

Window sizes (txt file) - this file is needed only when analyzing the data with software other than Spectronaut™ Pulsar

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