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scan-graph

scan_graph is a simple Python 3.0 project that shows how to extract a particular MS/MS scan out of a Thermo .raw file and generate an annotated graph for that scan using an assigned peptide sequence. This action reads the .raw file directly and it does not require performing an intermediate file conversion to some open text format, e.g. mzML or MGF.

There are three files:

  1. scan_graph.py - contains methods used to extract a scan from a .raw file and to generate lists of annotation peaks
  2. scan_graph_test.py - a demonstration of how to use the methods in scan_graph.py
  3. 9102-NGKITSIVKDSSAARNG.png - a sample PNG generated using scan_graph_test.py

Access to .raw files uses pymsfilereader, so you must install this package using the instructions at https://github.com/frallain/pymsfilereader. This package is only available for Windows, because accessing the files requires using a COM interface supplied by Thermo.

To run scan_graph_test.py, you will need an accessible .raw data file. In the code, a data file is specified by the path variable:

path = 'PXD018998\\01_001815W_KLH_2.raw'
  1. place scan_graph.py and scan_graph_test.py in a new directory;
  2. create the subdirectory PXD018998;
  3. grab the appropriate .raw from ftp://massive.ucsd.edu/MSV000085375/raw/01_001815W_KLH_2.raw;
  4. place 01_001815W_KLH_2.raw into PXD018998;
  5. from the command line, change into the directory containing the scripts and run > python scan_graph_test.py

As written, for the given example, scan_graph_test.py will annotate:

  1. a, b, b-NH3, b-H2O, y, y-NH3 and y-H2O ions for z = 1, 2 & 3;
  2. the parent ion as well as the parent -H2O & -2H2O (z=3); and
  3. immonium ions for each of the amino acids in the peptide sequence.

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