MS-DAS documentation

Motivation

MS-DAS stands for Mass Spectrometry Data AnalysiS. MS-DAS is a Python package that provides tools to read, manipulate and visualise Mass Spectrometry measurements. MS-DAS is not about pre-processing (at the spectra level) but rather focuses on providing tools to get more insights about relation between the peptides (e.g., for logical modeling).

MSDAS was designed to analysis a specific data set (YEAST) with a specific format. In this package, we try to enforce a common data structure so as to write all the pertinent tools only once.

MSDAS allows one to

1. read some Mass Spectrometry data stored in excel files
2. Align several files in a single data structure (dataframe).
3. Add annotations using UniProt service (sequence, protein, go terms)
4. Cluster the data if required
5. Creation of prior knowledge networks using phosphogrid and uniprot services
6. Export of the data into MIDAS format
7. Understanding the Quality of the data (if replicates are available)
8. Descriptive analysis is also possible at different level.

Installation

From the source file, type:

python setup.py install

If installing globally, you may need root permission (e.g., sudo access)

MS-DAS relies on standard libraries (e.g., numpy, matplotlib, pandas, networkx) and bioservices, which is also available on pypi website.

If the command above does not succeed, it may be related to one of the dependencies that failed to be installed, in which case you will need to install them manually. We would recommend to install NumPy first. Others should then work out of the box. You can install all those packages using pip, for instance:

pip install numpy

User guide

• 1. QuickStart
  • 1.1. Reading data into a dataframe
  • 1.2. Conventions
  • 1.3. Read a simple data set
  • 1.4. Read several files: the alignment class.
  • 1.5. Debugging and verbosity
  • 1.6. More about manipulating the dataframe
  • 1.7. Clustering of peptides
• 2. Building PKN
• 3. NoteBooks

References

• 1. Modules
  • 1.1. Alignment
  • 1.2. Cluster measurements with clustering module
  • 1.3. yeast data to PKN and MIDAS
  • 1.4. PKN construction
  • 1.5. Reading files with MassSpecReader (readers module)
  • 1.6. Handling replicates with MassSpecReplicates (replicates modules)
  • 1.7. psites
  • 1.8. tools (modification)
  • 1.9. annotations

Others