compomics-utilities protocols

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compomics-utilities specifications

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Unique identifier OMICS_04545
Name compomics-utilities
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for compomics-utilities

compomics-utilities in pipeline

2017
PMCID: 5466729
PMID: 28615994
DOI: 10.1186/s12953-017-0119-z

[…] of analysis available in the data files. post-translational modification localisations were scored using the d-score [] and the phosphors score [] with a threshold of 95.0 as implemented in the compomics-utilities package []. protein identification reports were exported in .xlsx format for evaluation and curation in excel spreadsheet. only proteins identified with 2 or more validated […]


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compomics-utilities in publications

 (5)
PMCID: 5466729
PMID: 28615994
DOI: 10.1186/s12953-017-0119-z

[…] of analysis available in the data files. post-translational modification localisations were scored using the d-score [] and the phosphors score [] with a threshold of 95.0 as implemented in the compomics-utilities package []. protein identification reports were exported in .xlsx format for evaluation and curation in excel spreadsheet. only proteins identified with 2 or more validated […]

PMCID: 5447515
PMID: 28580409
DOI: 10.1016/j.dib.2017.04.058

[…] and are available in and for all databases searched. post-translational modification localizations were scored using the d-score and the a-score with a threshold of 95.0 as implemented in the compomics-utilities package . an a-score above 95.0 was considered a confident localization. the mass spectrometry data along with the identification results have been deposited […]

PMCID: 5802045
PMID: 29450146
DOI: 10.1016/j.biopen.2017.03.001

[…] for all databases searched in the data in brief article . post-translational modification localizations were scored using the d-score and the a-score with a threshold of 95.0 as implemented in the compomics-utilities package ., the mass spectrometry raw data files along with the identification results have been deposited to the proteomexchange consortium via the pride partner repository […]

PMCID: 4955376
PMID: 27493641
DOI: 10.3389/fmicb.2016.01103

[…] and proteins were validated at 1% fdr estimated using the decoy hit distribution. post-translational modification localizations were scored using the d-score (vaudel et al., ) as implemented in the compomics-utilities package (barsnes et al., )., the mass spectrometry data, along with the peptideshaker identification results, have been deposited to the proteomexchange consortium (vizcaĆ­no et […]

PMCID: 4488739
PMID: 26110586
DOI: 10.3390/v7062772

[…] false discovery rate (fdr) estimated using the decoy hit distribution. post-translational modification localizations were scored using the d-score [] and the phosphors score [] as implemented in the compomics-utilities package []. the mass spectrometry data along with the identification results have been deposited to the proteomexchange consortium [] via the pride partner repository []., […]


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compomics-utilities institution(s)
Proteomics Unit, Department of Biomedicine, University of Bergen, Norway

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