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Update peptides_proteins.rst #432

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114 changes: 69 additions & 45 deletions docs/source/user_guide/peptides_proteins.rst
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Expand Up @@ -331,56 +331,80 @@ an influence on :py:meth:`~.AASequence.getMonoWeight` and :py:meth:`~.AASequence
Applying Fixed or Variable Modifications to Sequences
*****************************************************

In this tutorial, we will cover a step-by-step guide on how to use the pyopenms library to generate modified peptides from a given amino acid sequence.
In this tutorial, we will cover a step-by-step guide on how to use the `pyopenms` library to generate modified peptides from a given amino acid sequence.

.. code-block:: python
:linenos:
import pyopenms as poms

# Create an amino acid sequence using the fromString() method of the AASequence class.
# In this example, we will use the amino acid sequence "TESTMTECSTMTESTR"
sequence = poms.AASequence.fromString("TESTMTECSTMTESTR")

# We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively.
variable_mod_names = [b"Oxidation (M)"]
fixed_mod_names = [b"Carbamidomethyl (C)"]

# We then use the getModifications() method of the ModifiedPeptideGenerator class to get the modifications for these names.
variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names)
fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names)

# Apply the fixed modifications to the amino acid sequence
poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence)

# Define the maximum number of variable modifications allowed
max_variable_mods = 1

# Generate the modified peptides
peptides_with_variable_modifications = []
keep_unmodified_in_result = False
poms.ModifiedPeptideGenerator.applyVariableModifications(variable_modifications, sequence, max_variable_mods,
peptides_with_variable_modifications,
keep_unmodified_in_result)

# Print the modified peptides generated using Fixed modifications and their mono-isotopic mass.
print("Fixed:", sequence.toString())
print("Mono-isotopic mass:", sequence.getMonoWeight())

# Print the modified peptides generated using variable modifications and their mono-isotopic mass.
for peptide in peptides_with_variable_modifications:
print("Variable:", peptide.toString())
print("Mono-isotopic mass:", peptide.getMonoWeight())


import pyopenms as poms

Create an amino acid sequence using the `fromString()` method of the `AASequence` class. In this example, we will use the amino acid sequence "TESTMTECSTMTESTR".

.. code-block:: python

sequence = poms.AASequence.fromString("TESTMTECSTMTESTR")

We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively.

.. code-block:: python

variable_mod_names = [b"Oxidation (M)"]
fixed_mod_names = [b"Carbamidomethyl (C)"]

We then use the `getModifications()` method of the `ModifiedPeptideGenerator` class to get the modifications for these names.

.. code-block:: python

variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names)
fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names)

Apply the fixed modifications to the amino acid sequence.

.. code-block:: python

poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence)

Define the maximum number of variable modifications allowed.

.. code-block:: python

max_variable_mods = 1

Generate the modified peptides.

.. code-block:: python

peptides_with_variable_modifications = []
keep_unmodified_in_result = False
poms.ModifiedPeptideGenerator.applyVariableModifications(variable_modifications, sequence, max_variable_mods,
peptides_with_variable_modifications,
keep_unmodified_in_result)

Print the modified peptides generated using Fixed modifications and their mono-isotopic mass.

.. code-block:: python

print("Fixed:", sequence.toString())
print("Mono-isotopic mass:", sequence.getMonoWeight())

Print the modified peptides generated using variable modifications and their mono-isotopic mass.

.. code-block:: python

for peptide in peptides_with_variable_modifications:
print("Variable:", peptide.toString())
print("Mono-isotopic mass:", peptide.getMonoWeight())

The above code outputs:

.. code-block:: output
.. code-block:: python

Fixed: TESTMTEC(Carbamidomethyl)STMTESTR
Mono-isotopic mass: 1850.7332409542007
Variable: TESTMTEC(Carbamidomethyl)STM(Oxidation)TESTR
Mono-isotopic mass: 1866.7281559542005
Variable: TESTM(Oxidation)TEC(Carbamidomethyl)STMTESTR
Mono-isotopic mass: 1866.7281559542005

Fixed: TESTMTEC(Carbamidomethyl)STMTESTR
Mono-isotopic mass: 1850.7332409542007
Variable: TESTMTEC(Carbamidomethyl)STM(Oxidation)TESTR
Mono-isotopic mass: 1866.7281559542005
Variable: TESTM(Oxidation)TEC(Carbamidomethyl)STMTESTR
Mono-isotopic mass: 1866.7281559542005


Proteins and :term:`FASTA` Files
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