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SpectraST specifications

Information


Unique identifier OMICS_02461
Name SpectraST
Alternative name Spectra Search Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Spectra Search Tool

SpectraST citations

 (37)
library_books

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc STAMS2)

2018
PLoS Negl Trop Dis
PMCID: 5897034
PMID: 29608573
DOI: 10.1371/journal.pntd.0006351

[…] ins (). Each T. cruzi strain was processed and acquired in four biological replicates. MS/MS spectra acquired from three replicates of each DTU were used to build the reference spectral library using SpectraST software []. Following the construction of the reference MS/MS library, proteins from unknown T. cruzi strain samples were extracted and digested with trypsin before being analyzed by nLC-MS […]

library_books

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

2018
Sci Rep
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] ophet and combined with iProphet. Mayu was used to estimate iProphet probabilities to control for protein identification false discovery rate (FDR <1%). The final spectral library was assembled using SpectraST by retaining spectra above iProphet FDR controlled cutoff and normalizing chromatography to iRT peptide retention time reference. SpectraST output was then converted to tsv format suitable f […]

library_books

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

2017
Nat Commun
PMCID: 5663699
PMID: 29089484
DOI: 10.1038/s41467-017-01422-6

[…] ne was set as fixed modification. The light version of the raw spectral library was generated from all valid peptide spectrum matches and then refined into the non-redundant consensus libraries using SpectraST. Using the spectrast2tsv.py function in OpenSWATH, we then generated both the light and heavy MS assays as the final library constructed from top 3–6 most intense fragments with Q3 range fro […]

library_books

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host pathogen interactions

2017
Sci Rep
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] SWATHTM, HRM-MSTM) to perform relative and absolute quantification of proteins. Furthermore, shotgun data analyses using peptide fragment spectral libraries and spectral library search tools such as SpectraST rely on high-quality spectral data and can outperform sequence-based database searches in terms of speed, sensitivity, and specificity. In the present study, we identified and quantified on […]

call_split

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

2017
Nat Methods
PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398
call_split See protocol

[…] ated from the spectra collected by six LC-MS/MS runs in DDA mode of the identical unfractionated HEK-293 tryptic digest, as described previously.Combined human + M. tuberculosis library: Based on the SpectraST consensus library of the CAL and the M. tuberculosis, libraries, we generated a merged library by appending the M. tuberculosis to the CAL library using SpectraST (TPP 5.0). The protein iden […]

library_books

Exposure to the Epstein–Barr Viral Antigen Latent Membrane Protein 1 Induces Myelin Reactive Antibodies In Vivo

2017
Front Immunol
PMCID: 5498468
PMID: 28729867
DOI: 10.3389/fimmu.2017.00777

[…] peptides were synthesized (Shanghai Ruifu Chemical Co., Ltd.), and their MS2 spectra were recorded. Spectral libraries were created based on mass-spectrometrical analysis of the synthetic peptides by SpectraST (Institute for Systems Biology, USA). Identifications of spectra from experimental samples were repeated against these spectral libraries by SpectraST. In addition, six of these peptides wer […]

Citations

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SpectraST institution(s)
Institute for Systems Biology, Seattle, WA, USA

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