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iSanXoT-1.0.1
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@jmrodriguezc jmrodriguezc released this 22 May 21:31
· 171 commits to master since this release
1.0.1
e8905a3

1.0.1

DATE: 2022_05

Highlights

  • New general adapter to handle the results from proteomics pipelines: TPP, FragPipe, MaxQuant, Proteome Discoverer, etc.

  • New CNIC adapter to habdles the results from search engines and to calculate the pRatio, add the quantificacions, and calculate the most probable protein.

  • LEVEL_CALIBRATOR accepts the K-constant, the variance, and 'More params'

  • iSanXoT Wiki: https://github.com/CNIC-Proteomics/iSanXoT/wiki

Changes in the Graphical User Interface

  • New General Adapter to handle the results from proteomics pipelines: TPP, FragPipe, MaxQuant, ProteomeDiscoverer, etc.

  • New CNIC adapter to habdles the results from search engines and to calculate the pRatio, add the quantificacions, and calculate the most probable protein.

  • We have created some case studies to ilustrade the type of workflows:

    • WSPP: Work by González-Amor M, et al. Cardiovasc Res. 2021
      • WSPP step by step without asterisks (the jack of all trades)
      • Report:
        • Npep2prot_Quanprot: Zq, Nq(npeptides/prot)
    • WSPP-SBT: Work by García-Marqués F, et al. Mol Cell Proteomics. 2016:
      • Biology Systems: WSPP-SBT
      • Report using the asterisk (the jack of all trades)
        • Npep2prot_Quanprot: Zq, FDRq, Nq(npeptides/prot)
        • Nprot2cat_Quancat: Zc, FDRc, Nc(nprots/cat)
        • Zprot2cat_Quanprot_Quancat: Zq, Zc
    • WSPP_NORCOMBINE_RATIOS_SBT: Work by González-Amor M, et al. Cardiovasc Res. 2021
      • Report using the asterisk (the jack of all trades)
        • Npep2prot_Quanprot: Zq, FDRq, Nq(npeptides/prot)
      • Report using the asterisk (the jack of all trades) (1 sample)
        • Npep2prot_Quanprot: Zq, FDRq, Nq(npeptides/prot)
        • Nprot2cat_Quancat: Zc, FDRc, Nc(nprots/cat)
        • Zprot2cat_Quanprot_Quancat: Zq, Zc
      • Report produced by the merge of the sample reports with the ratios sample report (SBT)
    • WSPP_PTM: Work by Bonzon-Kulichenko E, et al. J Proteomics. 2020
      • WSPP step by step using asterisks (the jack of all trades)
      • Report using the asterisk (the jack of all trades)
        • Npep2prot_Quanprot: Zq, FDRq, Nq(npeptides/prot)
        • Npep2prot_Quanprot: Zpq, FDRpq, Ns(nscans/pep)

  • 'More params", the 'more params' has been improved.

  • LEVEL_CALIBRATOR accepts the K-constant, the variance, and 'More params'.

Changes in the Code Workflow

  • TABLETOCFG:

    • Fixing the file that forces the variance in the integrations.
    • Print all processes but forced or not.

  • SANSON: Fixing a bug in the filter of SANSON. The filter needs the parenthsis:
    ([FDR] < 0.05) & ([n_rel] >= 10) & ([n_rel] <= 100)

  • Integrations: force the parameters and create a file with the variance when the vatiance has been forced by the user in the task-table.

  • RELS_CREATOR: Admits the ID-q.tsv files as default.

  • New general adapter to handle the results from proteomics pipelines: TPP, FragPipe, MaxQuant, Proteome Discoverer, etc.

  • Improved the program that reports the integrated variances.

  • New program that reports the K-constant and the graphs of calibration.

  • New program that retrieves the times of workflow execution.

  • Fixing a problem with the Linux and Mac distribution.

Comments:

  • In Create new project, in the first menu you should put Name of the Project Folder and the second Path to locate the Project Folder.

  • In Open Project, change to Open Project Folder.

  • In project logs table it should be indicated (press the process to see the workflow logs).

  • In workflow logs it should be indicated (press the command to see the command logs).

  • Instead of Start, put Save and Run.

  • Menu name to Project.

  • Change the 'Adapter' tab to 'Input File'.

  • The getVariances program will return "sample/integration/Variance/TotNElems/ElemExcluded/IntegratedNElems..."

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