toolkit

iPhos Toolkit

The iPhos toolkit processes the LC-MS data in the standard format of mzXML. Hence raw LC-MS data are required to be converted first. And the overall workflow of iPhos-facilitated phosphoproteome investigation can be found in the "About iPhos" page.

We have prepared testing sample data for iPhos Peak Extraction Assister , iPhos module-1, iPhos Module-2 and iPhos Module-3.

The iPhos toolkit

The iPhos tookit includes one assister and three modules.
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*
indicates required field)

  • iPhos Peak Extraction Assister is a stand-alone software to be run on the users' personal computers. It can be donwloaded here.
  • Online tutorial for iPhos Peak Extraction Assister
  • flow
  • This is a tool to automate the batch mode peak extraction using the default peak extraction tool msInspsect.
  • To use the iPhos Peak Extraction Assister, users are required to install JAVA on the their personal computers. JAVA JRE can be downloaded on the download page of Oracle or here.
  • iPhos Peak Extraction Assister can be run on the Microsoft Windows system.

Peak Selection Parameters (w/o AP)

Top N intensive Peaks
*

Peak Selection Parameters (w AP)

Top N intensive Peaks
*

Mass Shift Calculation Parameters

Mass Delta (Da)
*

Maximal Modificaion Number
*

Minimum Charge State
*

Mass Tolerance (Da)
*

Retention Time Tolerance (min)
*

Headers in the Peak List Files

m/z
*

Charge State
*

Retention Time
*

Peak Intensity
*

Scan Number
Mass

Input Peak List Files (w/o AP)
*

File (A)
File (B)
File (C)
File (D)
File (E)
File (F)

Input Peak List Files (w AP)
*

File (1)
File (2)
File (3)
File (4)
File (5)
File (6)



Uploaded Peak List Files (You can adjust the parameter and directly use "Find Mass Shift.")

Peak list files w/o AP :
    Peak list files w AP :

      Download Result Files

        m/z Segment File Formation Parameters

        Peptide Elution Start (min)
        *

        Peptide Elution End (min)
        *

        Percentage of Peptides within One Segment (%)
        *

        Extra Retention Time Tolerance of Segment Files (min)
        *

        Inclusion List Generation Parameters

        Round Off Decimal Place
        *

        .csv Files from iPhos Module-1

        Control Group
        *
        File
        Treatment Group
        File

        Download Result Files

          Information Integration Parameters

          Minimum Peptide Score
          *

          m/z Tolerance (Da)
          *

          Retention Time Tolerance
          (min)
          *

          Phosphorylation Filter
          *



          Headers in the Quantification Results

          m/z
          *

          Charge State
          *

          Retention Time
          *

          Intensity Ratio
          *

          Highest Mean Condition
          Statistic p Value

          Input Peptide Identification Files (.xml)

          File
          *

          Input Quantification File

          File
          *


          Download Result Files