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Spectronaut specifications


Unique identifier OMICS_06206
Name Spectronaut
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Windows
Programming languages C#
License Commercial
Computer skills Advanced
Stability Stable
Maintained No


No version available

Spectronaut citations


Mutations in the pantothenate kinase of Plasmodium falciparum confer diverse sensitivity profiles to antiplasmodial pantothenate analogues

PLoS Pathog
PMCID: 5882169
PMID: 29614109
DOI: 10.1371/journal.ppat.1006918

[…] rther 20 min. The mass spectrometer was operated in a data-independent acquisition (DIA) mode with a 25-fixed-window setup of 24 m/z effective precursor isolation over the m/z range of 375–975 Da.For Spectronaut processing, raw files were loaded into Spectronaut (version 11, Biognosys) with an in-house P. falciparum-infected red blood cell library and default settings. Briefly, RT prediction type […]


Characterization of increasing stages of invasiveness identifies stromal/cancer cell crosstalk in rat models of mesothelioma

PMCID: 5893242
PMID: 29662647
DOI: 10.18632/oncotarget.24632

[…] Peak extraction of the SWATH data was performed using either the Spectronaut software (ver 8.0, Biognosys, Switzerland) or SWATH micro App embedded in PeakView (ver2.0, Sciex). SWATH data were processed with default settings in Spectronaut. Reference peptides from […]


Cost effective generation of precise label free quantitative proteomes in high throughput by microLC and data independent acquisition

Sci Rep
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] ng data using three publicly available spectral libraries generated by combining multiple tissues and fractionation or by repetitive injection of tissue-specific cell digests of HEK293 or HeLa cells (Spectronaut repository). MicroLC-SWATH-MS achieved quantification of 3951 ± 205, 1832 ± 74 and 2007 ± 63 proteins, respectively, out of single-injections of the unfractionated K562 protein digest, wit […]


Spatial Tissue Proteomics Quantifies Inter and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)*

PMCID: 5880102
PMID: 29363612
DOI: 10.1074/mcp.RA117.000189

[…] tions; mass tolerance of 10ppm (precursor ions) and 0.02 Da (fragment ions); minimal peptide length of 7 amino acids. The false discovery rate was set to < 0.01. The spectral library was generated in Spectronaut (Biognosys AG, Schlieren, Switzerland) using default settings.DIA files were searched in Spectronaut against the generated spectral library using default settings. For quantification only […]


Optimization of Experimental Parameters in Data Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results*

PMCID: 5724188
PMID: 29070702
DOI: 10.1074/mcp.RA117.000314

[…] DIA data were analyzed with Spectronaut 11, a mass spectrometer vendor independent software from Biognosys, Schlieren, Switzerland. The default settings were used for targeted analysis of DIA data in Spectronaut except the decoy […]


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

Nat Methods
PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398

[…] cumulation of false positives over a large number of samples. The error rate control strategies we have described are implemented and available in an updated PyProphet version () and are available in Spectronaut 11. Future developments might extend the statistical models to adjust probabilities for the detection of peptides and inference of proteins across multiple runs to improve detection sensit […]


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