MS Data Miner protocols

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MS Data Miner specifications

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Unique identifier OMICS_13914
Name MS Data Miner
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 1.3.0
Stability Stable
Maintained Yes

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Publication for MS Data Miner

MS Data Miner in pipeline

2015
PMCID: 4665887
PMID: 26628894
DOI: 10.1186/s12953-015-0084-3

[…] at 0.01, matched rho was 0.7, xic threshold was 0.1, isolated precursor threshold was set at 0.5 and normalization set to median. mascot distiller results were exported to xml files, imported into ms data miner v.1.2.0 (http://sourceforge.net/p/msdataminer []) and exported into excel reports. keratin was excluded as a general contaminant and a fold regulation threshold of 1.3 was selected […]


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MS Data Miner in publications

 (14)
PMCID: 5597892
PMID: 28873961
DOI: 10.1093/gigascience/gix057

[…] as described for digestive fluid samples, except that the mus musculus sequences were not interrogated. this dataset contains 9224 ms/ms queries. all obtained results were subsequently parsed using ms data miner v. 1.3.0 [], and protein hits were only accepted if they were identified based on 2 unique peptides. semi-quantitative proteomics data were obtained using the empai-values given […]

PMCID: 5350151
PMID: 28360834
DOI: 10.3389/fnmol.2017.00059

[…] peptides per protein. matched rho was set to 0.8, xic threshold to 0.3, and isolated precursor threshold to 0.7 and the peptide ion-score was set to 30. mascot distiller results were parsed using ms data miner v. 1.3 (dyrlund et al., ). the xic intensity of technical duplicates was averaged. quantified proteins showing at least a 5-fold up regulation when compared to the negative controls […]

PMCID: 4764196
PMID: 26758872
DOI: 10.1093/hmg/ddw001

[…] analyses. in addition, porcine tryptic peptides identical to human peptides were removed as porcine trypsin was used during the processing of the samples., all data were imported and processed in ms data miner v. 1.3.0 (). proteins were arranged on the basis of their exponentially modified protein abundance index values (empai). relative abundance was termed as the empai value […]

PMCID: 4691124
PMID: 26690411
DOI: 10.3390/ijms161226181

[…] da, respectively, and the instrument setting was specified as esi-quad-tof. the significance threshold (p) was set at 0.01, the ion score expect cut-off at 0.005. mascot results were parsed using ms data miner v. 1.3 []. mascot distiller 2.5.10 was used for the area-based xic quantification and the mascot search was performed using the same settings as for protein identification above except […]

PMCID: 4665887
PMID: 26628894
DOI: 10.1186/s12953-015-0084-3

[…] at 0.01, matched rho was 0.7, xic threshold was 0.1, isolated precursor threshold was set at 0.5 and normalization set to median. mascot distiller results were exported to xml files, imported into ms data miner v.1.2.0 (http://sourceforge.net/p/msdataminer []) and exported into excel reports. keratin was excluded as a general contaminant and a fold regulation threshold of 1.3 was selected […]


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MS Data Miner institution(s)
Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark; Center for Insoluble Protein Structures (inSPIN), Aarhus University, Denmark
MS Data Miner funding source(s)
This study was supported by the Danish Agency for Science, Technology, and Innovation and the Faculty of Science at Aarhus University.

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