DIA-SpecLib_Result_Summarizer

Extract the identified peptides and proteins from spectral library search of DIA proteomic data in Skyline

Note:

Prior to running the below command, in order to make sure that all the required columns are present in the Skyline output. The users can import the Skyline Report template provided here into Skyline and export their results.

How to use DIA-SpecLib_Result_Summarizer in Windows/Linux

>python extract_skyline_result.py -h
usage: extract_skyline_result.py [-h] -ip [-ip ...]

Extract and summarize Skyline results from DIA data analysis against spectral
library

positional arguments:
  -ip         Skyline output from DIA-Spectral Library search

optional arguments:
  -h, --help  show this help message and exit

iq input generator from Skyline search results

How to use iq_input_gen.py in Windows/Linux

>python iq_input_gen.py -h
usage: iq_input_gen.py [-h] -i [-i ...] -c [-c ...]

Generate a input matrix for the calculation of protein abundance using iq R
scrip

positional arguments:
  -i          Skyline output from DIA-Spectral Library search
  -c          A .txt file consisting the details of condition specific raw
              files used for the search

optional arguments:
  -h, --help  show this help message and exit