deamiDATE 1.0

deamiDATE 1.0 is a site-specific deamidation tool for palaeproteomics.

Given MaxQuant result output (in particular, the evidence.txt and peptides.txt files), it produces two graphs, one showing bulk deamidation, one showing site-specific deamidation. Deamidation is calculated per experiment, and per protein in experiment. If any filtering of experiments or proteins is required, it is recommended this is done before running deamiDATE.

Note: only tested on UNIX

Use:

• You will need Python 2.7
• You will need to install at least numpy and pandas (normally done with e.g. pip install numpy)

1. Make run.py executable, e.g. chmod +x run.py
2. Run program e.g. ./run.py with the following args:
   1. A directory containing at least evidence.txt and peptides.txt, e.g. ./run.py Test_Data
   2. [OPTIONAL] A text file containing a list (one per line) of relevant proteins to "filter in", e.g. ./run.py Test_Data Test_Data/protein_list.txt. Make sure you don't accidentally exclude all the proteins in the results. If you do this the program will crash with a mysterious warning that is not obvious.

Results will appear in the directory in argument 1.

There are two result plots

• One site specific
• One "bulk"

There are three result csv files

• One with site-specific results
• One with bulk results, averaged per protein and per sample
• One with bulk results, but with each deamidation measurement reported (no averaging)

Note: reported deamidation values are ALWAYS relative remaining N AND Q, NOT relative deamidation.

Common problems & solutions

Problems with evidence and peptide file path

• Change lines 22 and 23

Problems with finding Info/asn.csv or Info/gln.csv

• Change line 113 and 114

Filter out contaminants (default True)

• Change line 561 filter_con = False

Filter out reverse hits (default True)

• Change line 80 if intensity != "" and "REV" not in protein: to if intensity != "":

Show plots when created (default False)

• Change lines 563 and 564 show = True

Print csv of results (default True)

• Change lines 563 and 564 to_print = False

Change colormap

• In lines 384 - 390 change the colormap to another of your choice

Strange error appears: File "./run.py", line 237, in bulk_deam index = np.arange(len(relative[:,0])) IndexError: too many indices for array

• Make sure your protein list does not exclude all proteins in the results

Test Data

Test data is output of MaxQuant run on tapir files from: Welker, F. et al. Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates. Nature 522, 81–84 (2015).