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Update peptides_proteins.rst
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Ayesha-Feroz committed Mar 1, 2024
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Expand Up @@ -13,7 +13,6 @@ some commonly used operations like chemical formula, weight, and isotope distrib
The example below shows how amino acid sequences can be created and how basic mass calculations are conducted.

.. code-block:: python
:linenos:
import pyopenms as oms
Expand Down Expand Up @@ -96,7 +95,6 @@ The N- and C-Terminus as well as the residues themself can be modified.
The example below shows how to check for such modifications.

.. code-block:: python
:linenos:
seq = oms.AASequence.fromString("C[143]PKCK(Label:13C(6)15N(2))CR")
Expand Down Expand Up @@ -136,7 +134,6 @@ about :py:class:`~.EmpiricalFormula` to get accurate mass and isotope distributi
the amino acid sequence. But first, let's get the formula of peptide:

.. code-block:: python
:linenos:
seq = oms.AASequence.fromString("DFPIANGER")
seq_formula = seq.getFormula()
Expand All @@ -149,7 +146,6 @@ Isotope Patterns
We now want to print the coarse (e.g., peaks only at nominal masses) distribution.

.. code-block:: python
:linenos:
# print coarse isotope distribution
coarse_isotopes = seq_formula.getIsotopeDistribution(
Expand All @@ -165,7 +161,6 @@ But if we deal with very high resolution instruments, we still might want to cal
We use the :py:class:`~.FineIsotopePatternGenerator` in OpenMS to reveal these additional peaks:

.. code-block:: python
:linenos:
# print fine structure of isotope distribution
fine_isotopes = seq_formula.getIsotopeDistribution(
Expand All @@ -180,7 +175,6 @@ We use the :py:class:`~.FineIsotopePatternGenerator` in OpenMS to reveal these a
And plot the very similar looking distributions using standard ``matplotlib`` functionality:

.. code-block:: python
:linenos:
import math
from matplotlib import pyplot as plt
Expand Down Expand Up @@ -223,7 +217,6 @@ Fragment Ions
We can easily calculate different ion types for amino acid sequences:

.. code-block:: python
:linenos:
suffix = seq.getSuffix(3) # y3 ion "GER"
print("=" * 35)
Expand Down Expand Up @@ -264,7 +257,6 @@ peptide "DFPIAMGER" with an oxidized methionine. There are multiple ways to spec


.. code-block:: python
:linenos:
seq = oms.AASequence.fromString("PEPTIDESEKUEM(Oxidation)CER")
print(seq.toUnmodifiedString())
Expand Down Expand Up @@ -310,7 +302,6 @@ respectively, but ``".DFPIAMGER(Phospho)."`` will be interpreted as a
phosphorylation of the last arginine at its side chain:

.. code-block:: python
:linenos:
s = oms.AASequence.fromString(".(Dimethyl)DFPIAMGER.")
print(s, s.hasNTerminalModification())
Expand All @@ -334,43 +325,43 @@ 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.

.. 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())
import pyopenms as poms
# 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())
# 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())
The above code outputs:

.. code-block:: output
Expand All @@ -390,7 +381,6 @@ Protein sequences, can be loaded from and stored in :term:`FASTA` protein databa
The example below shows how protein sequences can be stored in :term:`FASTA` files and loaded back in pyOpenMS:

.. code-block:: python
:linenos:
bsa = oms.FASTAEntry() # one entry in a FASTA file
bsa.sequence = "MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGE"
Expand All @@ -409,7 +399,6 @@ The example below shows how protein sequences can be stored in :term:`FASTA` fil
Afterwards, the ``example.fasta`` file can be read again from the disk:

.. code-block:: python
:linenos:
entries = []
f = oms.FASTAFile()
Expand Down

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