msInspect protocols

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msInspect specifications

Information


Unique identifier OMICS_02384
Name msInspect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Martin McIntosh <>

Publication for msInspect

msInspect in pipelines

 (4)
2014
PMCID: 4192290
PMID: 25270759
DOI: 10.1186/s12870-014-0254-y

[…] generic format (mgf) using proteowizard [] and uploaded to the proteios software environment, prose []. mgf files were used for ms/ms identification, and mzml files for feature detection using msinspect []. peptide and protein identification were performed in mascot (http://www.matrixscience.com) and x!tandem (http://thegpm.org/tandem/) in a database consisting of all solanum proteins […]

2012
PMCID: 3311572
PMID: 22369182
DOI: 10.1186/1477-5956-10-13

[…] as a three-dimensional map that defines the lc-ms data. with an increasing interest in label-free quantification, several software tools have been made available for lc-ms data analysis including msinspect [], mzmine 2 [], progenesis lc-ms (nonlinear dynamics, united kingdom) [], and xcms []. while all tools are involved in preprocessing lc-ms data at some level [], they either […]

2009
PMCID: 2649809
PMID: 18984577
DOI: 10.1074/mcp.M800231-MCP200

[…] rate ≤0.05 were kept. lc-ms peptide intensity values for the peptides were normalized across runs, and peptide ratios were calculated. the amt database and matching were performed using the msinspect/amt software platform (, ). protein inference was performed using proteinprophet, and protein ratios were calculated as well. as with the lab 3 analysis, experiments were aligned using […]

2009
PMCID: 2766790
PMID: 20190954
DOI: 10.2174/138920209789177638

[…] be used to compare the performance of various peak picking algorithms., we tested the effect of various peak detection methods based on the peak list generated by the peak detection algorithms in msinspect, mzmine as well as that generated by the algorithm described in viper software which we implemented. the purpose of the test is to illustrate the effect of using various peak picking […]


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msInspect in publications

 (25)
PMCID: 5370288
PMID: 28367086
DOI: 10.7150/ijms.17792

[…] to the open file format mzxml via readw.exe, which is available in the trans-proteomic pipeline (tpp) platform (http://tools.proteomecenter.org/software.php). an open-source computer program, msinspect, was utilized to locate isotopes in the lc-ms data and assemble the isotopes into peptides. the msinspect software is distributed freely under an apache 2.0 license and is available […]

PMCID: 4934865
PMID: 27383761
DOI: 10.1371/journal.pone.0158844

[…] section) were set in the parent mass list for ltq-orbitrap ms., the raw data generated by an ltq-orbitrap ms were converted to an open file representation mzxml format using an open-source program, msinspect [], which was developed by the computational proteomics laboratory (cpl); operational analysis was then conducted (http://proteomics.fhcre.org) to acquire peak information after peak […]

PMCID: 4423582
PMID: 25951936
DOI: 10.1186/1471-2105-16-S7-S1

[…] compute a comparison between the (µ, τ, α) values for a centroid and the expected centroid values obtained from a heuristic isotopic envelope shape. note that isotopic trace extraction is ignored., msinspect [], another approach to isotopic envelope extraction, groups all coeluting signals and compares them to a simulated envelope calculated from a poisson distribution parameterized by m/z, […]

PMCID: 4324452
PMID: 25411686
DOI: 10.1021/pr500886y

[…] evaluating the shape of the peak and/or the distribution of nearby peaks (in both the m/z and retention time domains). for example, maxquant fits a gaussian curve to the raw m/z points in each peak. msinspect, openms, and dywave all employ wavelet transformations to assess the correlation between a model wavelet and spectral data. du and co-workers developed a similar algorithm called […]

PMCID: 4192290
PMID: 25270759
DOI: 10.1186/s12870-014-0254-y

[…] generic format (mgf) using proteowizard [] and uploaded to the proteios software environment, prose []. mgf files were used for ms/ms identification, and mzml files for feature detection using msinspect []. peptide and protein identification were performed in mascot (http://www.matrixscience.com) and x!tandem (http://thegpm.org/tandem/) in a database consisting of all solanum proteins […]


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msInspect institution(s)
LabKey Software, Seattle, WA, USA

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