iSanXoT-2.0.0

Date 📅 2024_11

Highlights

• The 'Experiment' column has been renamed as 'Batch'.

Changes in the Graphical User Interface

• Updated the description of the INTEGRATE module.

• Renamed the 'Experiment' column to 'Batch'

Changes in the Code Workflow

• Added functionality to print the sigmoide plots (with and without outliers) in the 'stats' folder.

Full Changelog: 1.2.13...2.0.0

iSanXoT-1.2.13

DATE: 2024_07

Highlights

• New version for the ProteinAssigner (v5). In this version, the changes are:

  • The parameter file has been transformed to INI format. This change was made because the ProteinAssigner is integrated into the PTM-workflow, and a consensus parameter file with the same format is required.
  • A preliminary filter for redundant proteins identified has been developed. This filter is applied before any other operation by the ProteinAssigner.

• New version of klibrate (v1.20):

  • Savitzky-Golay algortihm for smoothing has been included.

• Fixing a bug in the mz extraction for experiments with high resolution (greater than 30K), in the Quant package.

Changes in the Graphical User Interface

• Updated documentation.

• Modify the CNIC adapter to accept the new version of ProteinAssigner, which includes the preliminary filter.
  A new parameter has been added: "Preliminary Regex filter before any operation", applicable in both FASTA and column modes.

Changes in the Code Workflow

• Fixing a bug in reporter:

  • The X'inf and Winf variable are retrieved correctly.
  • Possible bug caused by dictionaries in Python.

• Fixing a bug in the mz extraction for experiments with high resolution (greater than 30K), in the Quant package.

• New version of klibrate (v1.20) has been developed:

  • Savitzky-Golay algortihm for smoothing has been applied. New parameters have been added:

   -S, --no-smoothing  Do not apply the Savitzky-Golay smoothing algorithm. It 
                       is applied by default.
   -t, --smoothing-window
                       The window size for the Savitzky-Golay smoothing 
                       algorithm. A larger window size will result in stronger 
                       smoothing. The window length must be less than or equal 
                       to the size of input. By default is length of integrated elements.
   -T, --smoothing-polynomial
                       The polynomial order for the Savitzky-Golay smoothing 
                       algorithm to fit the samples. A higher polynomial order 
                       can capture more complex patterns but may also introduce 
                       more artifacts.

iSanXoT-1.2.12

DATE: 2023_12

Highlights

• Fixing a bug in the 'New Project' window: The modal parameter for ElectronJS does not work in MacOSX version.

• Customize the context menu as the Copy and Paste commands do not work correctly in the MacOSX version.

• Open the processed project from the 'Project logs' table.

• The GitHub wiki has been closed.
  The updated documentation is available on the iSanXoT webpage: https://cnic-proteomics.github.io/iSanXoT

Changes in the Graphical User Interface

• Updated documentation.

iSanXoT-1.2.8

DATE: 2023_05

Highlights

• iSanXoT accepts projects with a huge number of experiments.

• The CNIC adaptor also includes the ProteinAssigner using the FASTA mode with the complete params (regex, len option, etc).

• The addQuantification module of CNIC adaptor accepts more types of TMTs (TMT16 and TMT18) for the isotopic correction.

• The REPORT module can filter OR conditions and it also merges multiple report tables at the same time.

• New documentation for the workflow samples.

iSanXoT-1.2.7

DATE: 2023_01

Highlights

• Improve the User Guide documentation in the iSanXoT help:

  • Update the documentation.
  • Divide by sections the documentation in multiple files.

• Update the iSanXoT Wiki:

  • Add the user guide files.
  • Add the Case studies.
  • Add the adaptor cases.

• NORCOMBINE:

  • Changes in the output file names.
  • Cardenio will recognize the experiment by the name of sample.

Changes in the Graphical User Interface

• Improve the User Guide documentation in the iSanXoT help.
  renamed: app/app/User_Guide.html -> app/app/User_Guide.htm
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  modified: app/app/renderer-process/imports.js
  deleted: app/app/sections/helps/help_cmds.html
  deleted: app/app/sections/helps/help_get-started.html
  deleted: app/app/sections/helps/help_intro.html
  deleted: app/app/sections/helps/help_wf-basic.html
  deleted: app/app/sections/helps/help_wf-lblfree.html
  deleted: app/app/sections/helps/help_wf-ptm.html

• LEVEL_CREATOR: Accepts the following operation for the ratio denominator: IS = if( or(count(a1…a4)=0, count(b1…b4)=0), '', Average(average(a1…a4), average(b1…b4)))
  [Intensity A_01 , Intensity A_02 , Intensity A_03 , Intensity A_04] , [Intensity B_01 , Intensity B_02 , Intensity B_03 , Intensity B_04]
  modified: app/resources/src/cmds/createLevels.py

Changes in the Code Workflow

• Come back in the 'problem': Fix a problem in ProteinAssigner when the pandas does not interpreted the Protein Accessions column as string.
  renamed: app/resources/src/cmds/extractQuant.py -> app/resources/src/cmds/extractquant.py
  modified: app/resources/src/cmds/ProteinAssigner_v3.py

• Reducing the path in the log report.
  modified: app/resources/wfs/table2cfg.py

• NORCOMBINE:

  • Changes in the file names.
    modified: app/resources/wfs/tpl_commands/norcombine.yaml
  • Cardenio will recognize the experiment by the name of sample.
    modified: app/resources/src/cmds/createCardenioTags.py

• Add the option to have multiple samaples in the inputs and the outpus.
  modified: app/resources/wfs/table2cfg.py

iSanXoT-1.0.2

DATE: 2022_05

Changes in the Graphical User Interface

• Adaptor: Bug fixed: the window in the adaptor was not displayed correctly.

• Adaptor: Allow the read of large files size.

Changes in the Code Workflow

• RELS_CREATOR: Now the delimiter in category files is '//'.

iSanXoT-1.0.1

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..."

iSanXoT-0.4.4

DATE: 2022_02

Highlights

• PROTEIN_ASSIGNER is the new Module for CNIC Adaptors.

• The REPORT module can retrieve the X'inf and Winf from the _lowerNormW files.

Changes in the Graphical User Interface

• We have included more details in the short description for the SBT module and RATIOS module.

• Create general adaptors for the search engines: Proteome Discoverer, MSFragger, Comet and MaxQuant.

• Fixing a minor problem loading the adaptors.

• PROTEIN_ASSIGNER is the new Module for CNIC Adaptors.

Changes in the Code Workflow

• Minor changes: changes the descrioption of ratios command.

• Now, the modules of adaptors are independent.

• TABLE2CFG: fixing a problem with the unique function. We want the unique list bbut without sort.

• General Adaptors for Proteome Discoverer, MSFragger, Comet, and MaxQuant:

  • These adaptors only create the columns: Experiment, Scan_Id, and Peptide_Id.
  • The calculation of Peptide_Id is without the DeltaMass forgetting the unimod file.

• CNIC Specific Adaptors:

  • These adaptors have the FDR calculation including the cXCorr (for PD).
  • There is a new Module for CNIC Adaptors: ProteinAssigner

• KLIBRATE: When the number of cycles in calibrate is exceeded, we can use k=600, var=0.04 by default. This is based on the values from PESA project:

• REPORT:
  • Bug fixed: the program does not retrieve the Xsup value.
  • The program can retrieve the X'inf and Winf from the _lowerNormW files.

iSanXoT-0.4.3

DATE: 2022_02

Changes in the Code Workflow

• Force the execution of Main-Input adaptor.

• Mysnake: we have developed a new way to obtain the list of processes.

iSanXoT-0.4.2

DATE: 2022_01

Changes in the Graphical User Interface

• The Adaptors tab has been renamed to 'Adaptor'.

• Fixing a bug in Comet Adaptor.

• Approximation to fix the problem when the administrator wants to install iSanXoT.

• Discard the close search words.

• Add list of scores that will use the FDR module adaptors by default.

• New validation of the workflow schema: Check if the input files exit in the table2cfg.

Changes in the Code Workflow

• Include some shell/batch scripts that prepares the environment for the build packages.

• Fixing a bug in the function that retrieves the folder name of jobs