Getting Started - PECAplus/Perseus-PluginPECA GitHub Wiki

Contents

Getting PluginPECA

Follow the instructions on Perseus Download and Installation Guide to install PERSEUS.

Follow the instructions on PluginPECA Installation to install PluginPECA.

Confirm that PluginPECA has been successfully installed by checking whether the PECA button is available under Processing

Quick Start with PECA Core

A quick start guide for PECA Core using Sample Files (also applies in a similar way to PECA-N, differing in that the GSA parameters and an extra Edge File parameter are required for PECA-N).

Loading the Input Matrix

  1. Select Generic Matrix Upload under Load

  1. Select the file path of N_Sample.txt for File option

  2. Insert the ENSG column under Text columns and insert the rest of the columns (i.e. R1t0, R1t0.5, ..., LFQ.intensity.8_30h_RS3) under Main columns.

  3. Press OK

Run PECA Core

  1. Select PECA Core under PECA button

  1. Fill out the PECA Core Parameters based on the Sample Parameters for PECA Core

  1. Press 'OK' to start running.
    NOTE THAT If you have any anti-virus software running, you might be prompted to give access to peca.exe, fdr.exe and gsa.exe. Please grant access to all of them.

  2. At the end of the processing, you will obtain two output matrices (if GSA Analysis option has been selected) as described by Output.
    The left output matrix is General Output and the right output matrix is GSA Output

Quick Start with PECA-pS

A quick start guide for PECA-pS using Sample Files (also applies in a similar way to PECA-R, differing in Data Input Form parameters that there is only one protein expression series for R as described here).

Loading the Input Matrix

  1. Select Generic Matrix Upload under Load

  1. Select the file path of pS_Sample.txt for File option

  2. Insert the Gene_Group column under Text columns and insert the rest of the columns (i.e. R1_LPS_0h, R1_LPS_01h, ..., HL_LPS_R2_12h) under Main columns.

  3. Press OK

Run PECA-pS

  1. Select PECA-pS under PECA button

  1. Fill out the PECA-pS Parameters based on the Sample Parameters for PECA-pS

  1. Press 'OK' to start running.
    NOTE THAT If you have any anti-virus software running, you might be prompted to give access to peca.exe, fdr.exe and gsa.exe. Please grant access to all of them.

  2. At the end of the processing, you will obtain one output matrices (if GSA Analysis option has not been checked) as described by Output.

If GSA Analysis option has been selected, you will obtain three output matrices.

The left output matrix is General Output, the middle output matrix is GSA Output on Synthesis Rates and the right output matrix is GSA Output on Degradation Rates