Data Types in pyXLMS

Most functions in pyXLMS return dictionaries with very specific structures, the most notable are crosslink dictionaries storing crosslink information, crosslink-spectrum-match dictionaries storing crosslink-spectrum-match information, and parser result dictionaries storing crosslinks and/or crosslink-spectrum-matches that have been parsed from a file. Each of these dictionaries is explained below.

Crosslink-Spectrum-Matches

Any method that returns or expects a crosslink-spectrum-match refers to a dictionary with the following keys and values, values that are not guaranteed may be None:

Key	Value Type	Value Guaranteed	Value Description
”data_type”	`Literal["crosslink-spectrum-match"]`	✅	Data type of the dictionary.
”completeness”	`Literal["full", "partial"]`	✅	Full crosslink-spectrum-matches have all their values set, partial crosslink-spectrum-matches have one or more missing values.
”alpha_peptide”	`str`	✅	The unmodified amino acid sequence of the alpha peptide.
”alpha_modifications”	`Dict[int, Tuple[str, float]]`	❌	The modifications of the alpha peptide given as a dictionary that maps peptide position (1-based) to modification given as a tuple of modification name and modification delta mass. N-terminal modifications are denoted with position 0. C-terminal modifications are denoted with position `len(peptide) + 1`. If the peptide is not modified an empty dictionary is given.
”alpha_peptide_crosslink_position”	`int`	✅	The position of the crosslinker in the sequence of the alpha peptide (1-based).
“alpha_proteins”	`List[str]`	❌	The accessions of proteins that the alpha peptide is associated with.
”alpha_proteins_crosslink_positions”	`List[int]`	❌	Positions of the crosslink in the proteins of the alpha peptide (1-based).
“alpha_proteins_peptide_positions”	`List[int]`	❌	Positions of the alpha peptide in the corresponding proteins (1-based).
“alpha_score”	`float`	❌	Identification score of the alpha peptide.
”alpha_decoy”	`bool`	❌	Whether the alpha peptide is from the decoy database or not.
”beta_peptide”	`str`	✅	The unmodified amino acid sequence of the beta peptide.
”beta_modifications”	`Dict[int, Tuple[str, float]]`	❌	The modifications of the beta peptide given as a dictionary that maps peptide position (1-based) to modification given as a tuple of modification name and modification delta mass. N-terminal modifications are denoted with position 0. C-terminal modifications are denoted with position `len(peptide) + 1`. If the peptide is not modified an empty dictionary is given.
”beta_peptide_crosslink_position”	`int`	✅	The position of the crosslinker in the sequence of the beta peptide (1-based).
“beta_proteins”	`List[str]`	❌	The accessions of proteins that the beta peptide is associated with.
”beta_proteins_crosslink_positions”	`List[int]`	❌	Positions of the crosslink in the proteins of the beta peptide (1-based).
“beta_proteins_peptide_positions”	`List[int]`	❌	Positions of the beta peptide in the corresponding proteins (1-based).
“beta_score”	`float`	❌	Identification score of the beta peptide.
”beta_decoy”	`bool`	❌	Whether the beta peptide is from the decoy database or not.
”crosslink_type”	`Literal["inter", "intra"]`	✅	If it is an inter- or intra-crosslink.
”score”	`float`	❌	Score of the crosslink-spectrum-match.
”spectrum_file”	`str`	✅	Name of the spectrum file the crosslink-spectrum-match was identified in.
”scan_nr”	`int`	✅	The corresponding scan number of the crosslink-spectrum-match.
”charge”	`int`	❌	The precursor charge of the corresponding mass spectrum of the crosslink-spectrum-match.
”retention_time”	`float`	❌	The retention time of the corresponding mass spectrum of the crosslink-spectrum-match in seconds.
”ion_mobility”	`float`	❌	The ion mobility or compensation voltage of the corresponding mass spectrum of the crosslink-spectrum-match.
”additional_information”	`Dict[str, Any]`	❌	A dictionary with additional information associated with the crosslink-spectrum-match.

Additional resources:

API Documentation of the crosslink-spectrum-match creator

Crosslinks

Any method that returns or expects a crosslink refers to a dictionary with the following keys and values, values that are not guaranteed may be None:

Key	Value Type	Value Guaranteed	Value Description
”data_type”	`Literal["crosslink"]`	✅	Data type of the dictionary.
”completeness”	`Literal["full", "partial"]`	✅	Full crosslinks have all their values set, partial crosslinks have one or more missing values.
”alpha_peptide”	`str`	✅	The unmodified amino acid sequence of the alpha peptide.
”alpha_peptide_crosslink_position”	`int`	✅	The position of the crosslinker in the sequence of the alpha peptide (1-based).
“alpha_proteins”	`List[str]`	❌	The accessions of proteins that the alpha peptide is associated with.
”alpha_proteins_crosslink_positions”	`List[int]`	❌	Positions of the crosslink in the proteins of the alpha peptide (1-based).
“alpha_decoy”	`bool`	❌	Whether the alpha peptide is from the decoy database or not.
”beta_peptide”	`str`	✅	The unmodified amino acid sequence of the beta peptide.
”beta_peptide_crosslink_position”	`int`	✅	The position of the crosslinker in the sequence of the beta peptide (1-based).
“beta_proteins”	`List[str]`	❌	The accessions of proteins that the beta peptide is associated with.
”beta_proteins_crosslink_positions”	`List[int]`	❌	Positions of the crosslink in the proteins of the beta peptide (1-based).
“beta_decoy”	`bool`	❌	Whether the beta peptide is from the decoy database or not.
”crosslink_type”	`Literal["inter", "intra"]`	✅	If it is an inter- or intra-crosslink.
”score”	`float`	❌	Score of the crosslink.
”additional_information”	`Dict[str, Any]`	❌	A dictionary with additional information associated with the crosslink.

Additional resources:

API Documentation of the crosslink creator

Parser Results

Any method that returns or expects a parser result (or parser_result) refers to a dictionary with the following keys and values, values that are not guaranteed may be None:

Key	Value Type	Value Guaranteed	Value Description
”data_type”	`Literal["parser_result"]`	✅	Data type of the dictionary.
”completeness”	`Literal["full", "partial", "empty"]`	✅	Full parser results have all their values set, partial parser results have one missing value, empty parser results contain no crosslink-spectrum-matches or crosslinks.
”search_engine”	`str`	✅	Name of the identifying crosslink search engine.
”crosslink-spectrum-matches”	`List[Dict[str, Any]]`	❌	List of parsed crosslink-spectrum-matches.
”crosslinks”	`List[Dict[str, Any]]`	❌	List of parsed crosslinks.

Additional resources:

API Documentation of the parser result creator