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QuasiTel specifications

Information


Unique identifier OMICS_33215
Name QuasiTel
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robbert Slebos

Publication for QuasiTel

QuasiTel citations

 (10)
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Probes for protein adduction in cholesterol biosynthesis disorders: Alkynyl lanosterol as a viable sterol precursor

2017
Redox Biol
PMCID: 5333532
PMID: 28258022
DOI: 10.1016/j.redox.2017.02.013
call_split See protocol

[…] ctrum match, 1 minimum spectra/peptide, 1 minimum spectra/match, 2 minimum distinct peptides/protein, 1 minimum additional peptide and 2 minimum spectra per protein. IDPicker reports were exported to QuasiTel to calculate enrichment factors between DMSO control and alkynyl-sterol samples. The cut-off for QuasiTel analysis used was greater than 2 of log2 (count1*/count2*), which count1*=total spec […]

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Cortactin promotes exosome secretion by controlling branched actin dynamics

2016
PMCID: 4949450
PMID: 27402952
DOI: 10.1083/jcb.201601025
call_split See protocol

[…] red using IDPicker () and Scaffold (http://www.proteomesoftware.com). Relative protein abundances and statistical significance of differences were evaluated via spectral counting techniques using the Quasitel program (). Quasitel uses a quasi-Poisson likelihood model to obtain multiple testing corrected p-value calculations, based on both spectral count consistency across biological replicates and […]

library_books

Proteomic analysis of colon and rectal carcinoma using standard and customized databases

2015
Sci Data
PMCID: 4477697
PMID: 26110064
DOI: 10.1038/sdata.2015.22

[…] e available through ProteomeXchange (Data Citation 13) or from the CPTAC data portal (cptac-data-portal.georgetown.edu/cptacPublic)). We compared the WHIM2 basal with the WHIM16 luminal samples using QuasiTel and selected 172 human proteins that distinguished the two xenograft types. Spectral counts for these proteins were at least 32-fold higher in one group over the other with an FDR- of less th […]

library_books

Co expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small cell lung cancer

2013
BMC Syst Biol
PMCID: 4029366
PMID: 24564859
DOI: 10.1186/1752-0509-7-S5-S1

[…] covery rate (FDR) [] below 5%. To compare protein expression differences between different histology groups (for example, SCLC vs. Normal), we applied our quasi-likelihood model and analysis software QuasiTel to analyze spectral count data []. The quasi-likelihood model, with no restriction on the distribution assumptions, is appropriate for modeling count data with overdispersion and/or underdisp […]

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A Multi Omic View of Host Pathogen Commensal Interplay in Salmonella Mediated Intestinal Infection

2013
PLoS One
PMCID: 3694140
PMID: 23840608
DOI: 10.1371/journal.pone.0067155
call_split See protocol

[…] observations are used as noted in text, figures, and tables. Statistical differences between control and infected spectral counts from mouse, Salmonella, and commensal proteins were identified using QuasiTel . The analysis was conducted in the R software environment . P-values adjusted for false discovery rate were used to filter the QuasiTel results. Early time points (days −1 and +1) were filte […]

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Global Stability of Plasma Proteomes for Mass Spectrometry Based Analyses*

2012
PMCID: 3433892
PMID: 22301387
DOI: 10.1074/mcp.M111.014340
call_split See protocol

[…] tween different runs was achieved by using the number of confident identifications as offset in the GLM. Proteins with GLM-generated p values of less than 0.05 were considered significantly different.Quasitel output generated at the peptide level guided in the selection of peptides to be monitored by LC-MRM-MS. The two most extreme conditions in the time point series and freeze thaw cycles were co […]

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QuasiTel institution(s)
Jim Ayers Institute for Precancer Detection and Diagnosis, Departments of Biostatistics, Biochemistry, Cancer Biology, Medicine, and Otolaryngology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Agricultural and Biosystems Engineering, University of Arizona, Tuscon, AZ, USA
QuasiTel funding source(s)
Supported by the National Cancer Institute Clinical Proteomic Technologies Assessment for Cancer program through National Institutes of Health Grant 1U24CA126479 and a generous gift from the Jim Ayers Foundation.

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