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).
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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™ Pulsar X offers novel workflows to significantly extend the number of research applications:
Spectronaut™ Pulsar X also includes new features that facilitate the data analysis through improved performance and visualization:
Spectronaut™ Pulsar analyzes raw data from a large variety of different methods:
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. Gas phase fractionation is supported.
Minimum: Windows 7 x64, CPU Intel ® Core™ CPU 2.7 GHz (quad core), HDD 200 GB free space, Memory 8 GB, Software .NET 4.5.
Recommended: Windows 7 x64 or higher, CPU Intel Core i7 4770, 3.4 GHz (octa core) or more, HDD 500 GB free space (SSD), Memory 16 GB or more, Software .NET 4.5 or higher.
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If you refer to Spectronaut™ algorithms in your research please cite:
Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011;8(5):430-5.
If you refer to the software package please cite:
Bruderer R, Bernhardt OM, Gandhi T, Miladinovic SM, Cheng LY, Messner S, et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues. Mol Cell Proteomics. 2015 Feb 27. pii: mcp.M114.044305.
FASTA of iRT peptides for shotgun search
Skyline Schema for exporting Spectronaut compatible libraries - simply add this schema to Skyline's report list
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
HEK293 demo data set
HEK cell line sample
Window sizes (txt file) - this file is needed only when analyzing the data with software other than Spectronaut™ Pulsar
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Can you explain the concept of Hybrid Libraries?
Hybrid Libraries are a combination of DIA and DDA libraries to maximize the proteome coverage beyond the core proteome. To minimize the mass spectrometer overhead time the DDA libraries are taken from resource data such as the Kim et. al data set.
Combining multiple libraries is well established, what is different with the Hybrid Libraries?
Spectronaut™ Pulsar X is to our knowledge the only software that combines precursor FDR, protein FDR and protein inference to control the data quality. Further, Spectronaut™ Pulsar X has implemented source specific iRT calibration to maximize the identifications and quantification quality.
Can you explain what you mean with spike in workflow?
In this workflow a set of stable isotope labelled peptides are spiked into the sample and analysed in DIA. Spectronaut™ Pulsar can process the data multi channel wise to display the heavy light ratios and the label free quantities in the same experiment. For human plasma and other body fluids Biognosys has recently launched PQ500 specifically for this workflow. Yet, any other panel can be used.
What is calibration carry-over for Host Cell Proteins (HCP)?
In this workflow the retention time calibration of the best run is used for all other runs. In an HCP run the best run is usually the run with the majority of the host cell proteins still in there.
If you have any further questions, please visit our Helpdesk at help.biognosys.com.
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