proforma - Proteoform and Peptidoform Notation ¶

ProForma is a notation for defining modified amino acid sequences using a set of controlled vocabularies, as well as encoding uncertain or partial information about localization. See ProForma specification for more up-to-date information.

Strictly speaking, this implementation supports ProForma v2.

Contents

proforma - Proteoform and Peptidoform Notation

Data Access ¶

parse() - The primary interface for parsing ProForma strings.

>>> parse("EM[Oxidation]EVT[#g1(0.01)]S[#g1(0.09)]ES[Phospho#g1(0.90)]PEK")
    ([('E', None),
      ('M', [GenericModification('Oxidation', None, None)]),
      ('E', None),
      ('V', None),
      ('T', [LocalizationMarker(0.01, None, '#g1')]),
      ('S', [LocalizationMarker(0.09, None, '#g1')]),
      ('E', None),
      ('S',
      [GenericModification('Phospho', [LocalizationMarker(0.9, None, '#g1')], '#g1')]),
      ('P', None),
      ('E', None),
      ('K', None)],
     {'n_term': None,
      'c_term': None,
      'unlocalized_modifications': [],
      'labile_modifications': [],
      'fixed_modifications': [],
      'intervals': [],
      'isotopes': [],
      'group_ids': ['#g1']})

to_proforma() - Format a sequence and set of properties as ProForma text.

Classes ¶

ProForma - An object oriented version of the parsing and formatting code, coupled with minimal information about mass and position data.

>>> seq = ProForma.parse("EM[Oxidation]EVT[#g1(0.01)]S[#g1(0.09)]ES[Phospho#g1(0.90)]PEK")
>>> seq
ProForma([('E', None), ('M', [GenericModification('Oxidation', None, None)]), ('E', None),
          ('V', None), ('T', [LocalizationMarker(0.01, None, '#g1')]), ('S', [LocalizationMarker(0.09, None, '#g1')]),
          ('E', None), ('S', [GenericModification('Phospho', [LocalizationMarker(0.9, None, '#g1')], '#g1')]),
          ('P', None), ('E', None), ('K', None)],
          {'n_term': None, 'c_term': None, 'unlocalized_modifications': [],
           'labile_modifications': [], 'fixed_modifications': [], 'intervals': [],
           'isotopes': [], 'group_ids': ['#g1'], 'charge_state': None}
        )
>>> seq.mass
1360.51054400136
>>> seq.tags
[GenericModification('Oxidation', None, None),
 LocalizationMarker(0.01, None, '#g1'),
 LocalizationMarker(0.09, None, '#g1'),
 GenericModification('Phospho', [LocalizationMarker(0.9, None, '#g1')], '#g1')]
>>> str(seq)
'EM[Oxidation]EVT[#g1(0.01)]S[#g1(0.09)]ES[Phospho|#g1(0.9)]PEK'

Dependencies ¶

To resolve PSI-MOD, XL-MOD, and GNO identifiers, psims is required. By default, psims retrieves the most recent version of each controlled vocabulary from the internet, but includes a fall-back version to use when the network is unavailable. It can also create an application cache on disk.

CV Disk Caching¶

ProForma uses several different controlled vocabularies (CVs) that are each versioned separately. Internally, the Unimod controlled vocabulary is accessed using Unimod and all other controlled vocabularies are accessed using psims. Unless otherwise stated, the machinery will download fresh copies of each CV when first queried.

To avoid this slow operation, you can keep a cached copy of the CV source file on disk and tell pyteomics and psims where to find them:

from pyteomics import proforma

# set the path for Unimod loading via pyteomics
proforma.set_unimod_path("path/to/unimod.xml")

# set the cache directory for downloading and reloading OBOs via psims
proforma.obo_cache.cache_path = "obo/cache/dir/"
proforma.obo_cache.enabled = True

Compliance Levels ¶

1. Base Level Support Represents the lowest level of compliance, this level involves providing support for:

[x] Amino acid sequences

[x] Protein modifications using two of the supported CVs/ontologies: Unimod and PSI-MOD.

[x] Protein modifications using delta masses (without prefixes)

[x] N-terminal, C-terminal and labile modifications.

[x] Ambiguity in the modification position, including support for localisation scores.

[x] INFO tag.

2. Additional Separate Support These features are independent from each other:

[x] Unusual amino acids (O and U).

[x] Ambiguous amino acids (e.g. X, B, Z). This would include support for sequence tags of known mass (using the character X).

[x] Protein modifications using delta masses (using prefixes for the different CVs/ontologies).

[x] Use of prefixes for Unimod (U:) and PSI-MOD (M:) names.

[x] Support for the joint representation of experimental data and its interpretation.

Top Down Extensions
- [ ] Additional CV/ontologies for protein modifications: RESID (the prefix R MUST be used for RESID CV/ontology term names)
- [x] Chemical formulas (this feature occurs in two places in this list).
Cross-Linking Extensions
- [ ] Cross-linked peptides (using the XL-MOD CV/ontology, the prefix X MUST be used for XL-MOD CV/ontology term names).
Glycan Extensions
- [x] Additional CV/ontologies for protein modifications: GNO (the prefix G MUST be used for GNO CV/ontology term names)
- [x] Glycan composition.
- [x] Chemical formulas (this feature occurs in two places in this list).
Spectral Support
- [x] Charge state and adducts
- [ ] Chimeric spectra are special cases.
- [x] Global modifications (e.g., every C is C13).

Functions ¶

pyteomics.proforma.parse(sequence)[source]¶

Tokenize a ProForma sequence into a sequence of amino acid+tag positions, and a mapping of sequence-spanning modifiers.

Note

This is a state machine parser, but with certain sub-state paths unrolled to avoid an explosion of formal intermediary states.

Parameters:	sequence (str) – The sequence to parse
Returns:	parsed_sequence (list[tuple[str, list[TagBase]]]) – The (amino acid: str, TagBase or None) pairs denoting the positions along the primary sequence modifiers (dict) – A mapping listing the labile modifications, fixed modifications, stable isotopes, unlocalized modifications, tagged intervals, and group IDs

pyteomics.proforma.to_proforma(sequence, n_term=None, c_term=None, unlocalized_modifications=None, labile_modifications=None, fixed_modifications=None, intervals=None, isotopes=None, charge_state=None, group_ids=None)[source]¶

Convert a sequence plus modifiers into formatted text following the ProForma specification.

Parameters:	sequence (list[tuple[str, TagBase]]) – The primary sequence of the peptidoform/proteoform to render n_term (Optional[TagBase]) – The N-terminal modification, if any. c_term (Optional[TagBase]) – The C-terminal modification, if any. unlocalized_modifications (Optional[list[TagBase]]) – Any modifications which aren’t assigned to a specific location. labile_modifications (Optional[list[TagBase]]) – Any labile modifications fixed_modifications (Optional[list[ModificationRule]]) – Any fixed modifications intervals (Optional[list[TaggedInterval]]) – A list of modified intervals, if any isotopes (Optional[list[StableIsotope]]) – Any global stable isotope labels applied charge_state (Optional[ChargeState]) – An optional charge state value group_ids (Optional[list[str]]) – Any group identifiers. This parameter is currently not used.
Returns:
Return type:	str

Helpers¶

pyteomics.proforma.set_unimod_path(path)[source]¶

Set the path to load the Unimod database from for resolving ProForma Unimod modifications.

Note

This method ensures that the Unimod modification database loads quickly from a local database file instead of downloading a new copy from the internet.

Parameters:	path (str or file-like object) – A path to or file-like object for the “unimod.xml” file.
Returns:
Return type:	`Unimod`

High Level Interface ¶

class pyteomics.proforma.ProForma(sequence, properties)[source]¶

Bases: object

Represent a parsed ProForma sequence.

The preferred way to instantiate this class is via the parse() method.

sequence¶

The list of (amino acid, tag collection) pairs making up the primary sequence of the peptide.

Type:	list[tuple[str, List[TagBase]]]

isotopes¶

A list of any stable isotope rules that apply to this peptide

Type:	list[StableIsotope]

charge_state¶

An optional charge state that may have been provided

Type:	int, optional

intervals¶

Any annotated intervals that contain either sequence ambiguity or a tag over that interval.

Type:	list[Interval]

labile_modifications¶

Any modifications that were parsed as labile, and may not appear at any location on the peptide primary sequence.

Type:	list[ModificationBase]

unlocalized_modifications¶

Any modifications that were not localized but may be attached to peptide sequence evidence.

Type:	list[ModificationBase]

n_term¶

Any modifications on the N-terminus of the peptide

Type:	list[ModificationBase]

c_term¶

Any modifications on the C-terminus of the peptide

Type:	list[ModificationBase]

group_ids¶

The collection of all groupd identifiers on this sequence.

Type:	set

mass¶

The computed mass for the fully modified peptide, including labile and unlocalized modifications. Does not include stable isotopes at this time

Type:	float

__init__(sequence, properties)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tags_by_id(tag_id, include_position=True)[source]¶

Find all occurrences of a particular tag ID

Parameters:	tag_id (str) – The tag ID to search for include_position (bool) – Whether or not to return the locations for matched tag positions
Returns:
Return type:	list[tuple[Any, TagBase]] or list[TagBase]

fragments(ion_shift, charge=1, reverse=None, include_labile=True, include_unlocalized=True)[source]¶

The function generates all possible fragments of the requested series type.

Parameters:	ion_shift (float or str) – The mass shift of the ion series, or the name of the ion series charge (int) – The charge state of the theoretical fragment masses to generate. Defaults to 1+. If 0 is passed, neutral masses will be returned. reverse (bool, optional) – Whether to fragment from the N-terminus (`False`) or C-terminus (`True`). If `ion_shift` is a `str`, the terminal will be inferred from the series name. Otherwise, defaults to `False`. include_labile (bool, optional) – Whether or not to include dissociated modification masses. Defaults to `True` include_unlocalized (bool, optional) – Whether or not to include unlocalized modification masses. Defaults to `True`
Returns:
Return type:	np.ndarray

Examples

>>> p = proforma.ProForma.parse("PEPTIDE")
>>> p.fragments('b', charge=1)
array([ 98.06004032, 227.1026334 , 324.15539725, 425.20307572,
        538.2871397 , 653.31408272])
>>> p.fragments('y', charge=1)
array([148.06043424, 263.08737726, 376.17144124, 477.21911971,
       574.27188356, 703.31447664])

classmethod parse(string)[source]¶

Parse a ProForma string.

Parameters:	string (str) – The string to parse
Returns:
Return type:	ProForma

Tag Types ¶

class pyteomics.proforma.TagBase(type, value, extra=None, group_id=None)[source]¶

Bases: object

A base class for all tag types.

type¶

An element of TagTypeEnum saying what kind of tag this is.

Type:	Enum

value¶

The data stored in this tag, usually an externally controlled name

Type:	object

extra¶

Any extra tags that were nested within this tag. Usually limited to INFO tags but may be other synonymous controlled vocabulary terms.

Type:	list

group_id¶

A short label denoting which group, if any, this tag belongs to

Type:	str or None

__init__(type, value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tag_type(tag_type)[source]¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

class pyteomics.proforma.TagTypeEnum[source]¶

Bases: enum.Enum

An enumeration.

Modification Tags¶

class pyteomics.proforma.MassModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.TagBase

A modification defined purely by a signed mass shift in Daltons.

The value of a MassModification is always a float

__init__(value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

class pyteomics.proforma.ModificationBase(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.TagBase

A base class for all modification tags with marked prefixes.

While ModificationBase is hashable, its equality testing brings in additional tag-related information. For pure modification identity comparison, use key to get a ModificationToken free of these concerns..

__init__(value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()[source]¶: Find the term and return it’s properties

class pyteomics.proforma.GenericModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()[source]¶: Find the term, searching through all available vocabularies and return the first match’s properties

class pyteomics.proforma.FormulaModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()[source]¶: Find the term and return it’s properties

class pyteomics.proforma.UnimodModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()¶: Find the term and return it’s properties

class pyteomics.proforma.PSIModModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()¶: Find the term and return it’s properties

class pyteomics.proforma.XLMODModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()¶: Find the term and return it’s properties

class pyteomics.proforma.GNOmeModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()¶: Find the term and return it’s properties

class pyteomics.proforma.GlycanModification(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.ModificationBase

__init__(value, extra=None, group_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

composition¶: The chemical composition shift this modification applies

definition¶

A dict of properties describing this modification, given by the providing controlled vocabulary. This value is cached, and should not be modified.

Returns:
Return type:	dict

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

id¶

The unique identifier given to this modification by its provider

Returns:
Return type:	str or int

key¶

Get a safe-to-hash-and-compare ModificationToken representing this modification without tag-like properties.

Returns:
Return type:	ModificationToken

mass¶

The monoisotopic mass shift this modification applies

Returns ——-float

name¶

The primary name of this modification from its provider.

Returns:
Return type:	str

provider¶

The name of the controlled vocabulary that provided this modification.

Returns:
Return type:	str

resolve()[source]¶: Find the term and return it’s properties

class pyteomics.proforma.ModificationToken(name, id, provider, source_cls)[source]¶

Bases: object

Describes a particular modification from a particular provider, independent of a TagBase’s state.

This class is meant to be used in place of a ModificationBase object when equality testing and hashing is desired, but do not want extra properties to be involved.

ModificationToken is comparable and hashable, and can be compared with ModificationBase subclass instances safely. It can be called to create a new instance of the ModificationBase it is equal to.

name¶

The name of the modification being represented, as the user specified it.

Type:	str

id¶

Whatever unique identifier the providing controlled vocabulary gave to this modification

Type:	int or str

provider¶

The name of the providing controlled vocabulary.

Type:	str

source_cls¶

A sub-class of ModificationBase that will be used to fulfill this token if requested, providing it a resolver.

Type:	type

__init__(name, id, provider, source_cls)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Label Tags¶

class pyteomics.proforma.InformationTag(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.TagBase

A tag carrying free text describing the location

__init__(value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

class pyteomics.proforma.PositionLabelTag(value=None, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.GroupLabelBase

A tag to mark that a position is involved in a group in some way, but does not imply any specific semantics.

__init__(value=None, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

class pyteomics.proforma.LocalizationMarker(value, extra=None, group_id=None)[source]¶

Bases: pyteomics.proforma.GroupLabelBase

A tag to mark a particular localization site

__init__(value, extra=None, group_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

find_tag_type(tag_type)¶

Search this tag or tag collection for elements with a particular tag type and return them.

Parameters:	tag_type (TagTypeEnum) – A label from `TagTypeEnum`, or an equivalent type.
Returns:	matches – The list of all tags in this object which match the requested tag type.
Return type:	list

Supporting Types ¶

class pyteomics.proforma.ModificationRule(modification_tag, targets=None)[source]¶

Bases: object

Define a fixed modification rule which dictates a modification tag is always applied at one or more amino acid residues.

modification_tag¶

The modification to apply

Type:	TagBase

targets¶

The list of amino acids this applies to

Type:	list

__init__(modification_tag, targets=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class pyteomics.proforma.StableIsotope(isotope)[source]¶

Bases: object

Define a fixed isotope that is applied globally to all amino acids.

isotope¶

The stable isotope string, of the form [<isotope-number>]<element> or a special isotopoform’s name.

Type:	str

__init__(isotope)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class pyteomics.proforma.TaggedInterval(start, end=None, tags=None, ambiguous=False)[source]¶

Bases: object

Define a fixed interval over the associated sequence which contains the localization of the associated tag or denotes a region of general sequence order ambiguity.

start¶

The starting position (inclusive) of the interval along the primary sequence

Type:	int

end¶

The ending position (exclusive) of the interval along the primary sequence

Type:	int

tags¶

The tags being localized

Type:	list[TagBase]

ambiguous¶

Whether the interval is ambiguous or not

Type:	bool

__init__(start, end=None, tags=None, ambiguous=False)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class pyteomics.proforma.ChargeState(charge, adducts=None)[source]¶

Bases: object

Describes the charge and adduct types of the structure.

charge¶

The total charge state as a signed number.

Type:	int

adducts¶

Each charge carrier associated with the molecule.

Type:	list[str]

__init__(charge, adducts=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Modification Resolvers¶

class pyteomics.proforma.ModificationResolver(name, **kwargs)[source]¶

Bases: object

__init__(name, **kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

parse_identifier(identifier)[source]¶

Parse a string that is either a CV prefixed identifier or name.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.

class pyteomics.proforma.GenericResolver(resolvers, **kwargs)[source]¶

Bases: pyteomics.proforma.ModificationResolver

__init__(resolvers, **kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

parse_identifier(identifier)[source]¶

Parse a string that is either a CV prefixed identifier or name.

Does no parsing as a GenericModification is never qualified.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.

class pyteomics.proforma.UnimodResolver(**kwargs)[source]¶

Bases: pyteomics.proforma.ModificationResolver

__init__(**kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

parse_identifier(identifier)¶

Parse a string that is either a CV prefixed identifier or name.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.

class pyteomics.proforma.PSIModResolver(**kwargs)[source]¶

Bases: pyteomics.proforma.ModificationResolver

__init__(**kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

parse_identifier(identifier)¶

Parse a string that is either a CV prefixed identifier or name.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.

class pyteomics.proforma.XLMODResolver(**kwargs)[source]¶

Bases: pyteomics.proforma.ModificationResolver

__init__(**kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

parse_identifier(identifier)¶

Parse a string that is either a CV prefixed identifier or name.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.

class pyteomics.proforma.GNOResolver(**kwargs)[source]¶

Bases: pyteomics.proforma.ModificationResolver

__init__(**kwargs)[source]¶: Initialize self. See help(type(self)) for accurate signature.

get_mass_from_glycan_composition(term)[source]¶

Parse the Byonic-style glycan composition from property GNO:00000202 to get the counts of each monosaccharide and use that to calculate mass.

The mass computed here is exact and dehydrated, distinct from the rounded-off mass that get_mass_from_term() will produce by walking up the CV term hierarchy. However, not all glycan compositions are representable in GNO:00000202 format, so this may silently be absent or incomplete, hence the double-check in get_mass_from_term().

Parameters:	term (psims.controlled_vocabulary.Entity) – The CV entity being parsed.
Returns:	mass – If a glycan composition is found on the term, the computed mass will be returned. Otherwise the `None` is returned
Return type:	float or `None`

get_mass_from_term(term, raw_mass)[source]¶

Walk up the term hierarchy and find the mass group term near the root of the tree, and return the most accurate mass available for the provided term.

The mass group term’s mass is rounded to two decimal places, leading to relatively large errors.

Parameters:	term (psims.controlled_vocabulary.Entity) – The CV entity being parsed.
Returns:	mass – If a root node is found along the term’s lineage, computed mass will be returned. Otherwise the `None` is returned. The mass may be
Return type:	float or `None`

parse_identifier(identifier)¶

Parse a string that is either a CV prefixed identifier or name.

Parameters:	identifier (str) – The identifier string to parse, removing CV prefix as needed.
Returns:	name (str, optional) – A textual identifier embedded in the qualified identifier, if any, otherwise `None`. id (int, optional) – An integer ID embedded in the qualified identifier, if any, otherwise `None`.