C-Seqer

A C++11 rewrite of the Python SweetSEQer algorithm. View the publication here.

This work is a derivative of the original SweetSEQer algorithm licensed to Oliver Serang (2012): https://pubmed.ncbi.nlm.nih.gov/23443135/

Requirements:

• Python 2.7 (for plotting)
  • Matplotlib 1.5.3
  • NetworkX 1.1
  • Numpy 1.16.6

Linux

• g++ 9.3.0 compiler
• gnu plot 5.2 patchlevel 8
• (If running in Ubuntu bash shell for Windows 10) Xming server 6.9.0.31 for display of charts

Windows

• MinGW compiler for C and C++

Compiling

C-SEQer uses the Cmake build system which makes compilation from source straightforward.

Cmake

1. Generate the Makefile (this will appear in the build/ directory):
       cmake .
2. Build the executable by executing from the build directory:
       Linux:       make Makefile
       Windows: mingw32-make -f Makefile

From Source

If compiling from source, navigate to the src/ directory with the following files:

• C-SEQER.cpp
• MGF.hpp
• main_functions.hpp
• DeNovo.hpp
• DiGraph.hpp
• dictionary.hpp
• (plot_glycan.py is only required when running the executable and passing in a positive print argument)

Execute g++ C-SEQER.cpp -o c-seqer.exe

Run:

Required files:

• executable
• .mgf file
• plot_glycan.py if plotting .png format figures

Example of execution command with parameters:

      ./c-seqer.exe 0.01 0.01 1 1 500 1 1 120810_JF_HNU142_5.mgf

Parameters

Run the executable with 8 parameters:

1. epsilon:         maximum absolute error between predicted and actual peak (in m/z)
2. lambda:         minimum peak intensity (relative to maximum peak intensity)
3. p:                    minimum length of inferred peptide sequence
4. g:                    minimum size of inferred glycan graph (including isotope peaks, not shown in graph)
5. tau:                 minimum m/z value to include in glycan
6. print output: either 0 (doesn't print text results) or 1 (prints text results for matches)
7. plot results:   either 0 (doesn't plot results) or 1 (interactively plots each matching spectrum
8. MGF file:        paths to an MGF files to process

Output

1. One .txt file with title of format <MGf file Name>_<epsilon>Da<lambda>int<g>g.txt

   • Contains a single line per valid spectrum (any spectrum containing glycan fragments meeting the user set p and g parameters) that is contained in the .mgf file, with the following data:
     • Spectrum charge
     • spectrum pepMass
     • spectrum rtInSeconds
     • charge state of spectrum for described fragment
     • start node of fragment
     • end node of fragment

2. Two .png files with the spectrum name as image title:

   1. one for the annotated spectrum
   2. another for the glycan graph