Description of the pyXLMS file format

Reading files with parser.read(*, engine="Custom") requires the following data format for crosslinks and crosslink-spectrum-matches. While the column names can be adjusted via the parameter column_mapping, the format of the columns needs to stay the same for successful parsing. Any column that is not required can be safely omitted. This format is also output by transform.to_dataframe().

For an extended description including additional examples please refer to here .

Crosslink-Spectrum-Matches

Data required for parsing crosslink-spectrum-matches:

Column Name	Required	Data Type	Example 1	Description
Alpha Peptide	✅	str	PEPKTIDE	Unmodified amino acid sequence of the alpha peptide in uppercase letters
Alpha Peptide Modifications	❌	str	(4:[DSS\|138.06808])	Modifications of the alpha peptide, see ➡️ Modification Encoding
Alpha Peptide Crosslink Position	✅	int	4	Position of the crosslinker in the alpha peptide (1-based)
Alpha Proteins	❌	str	G3ECR1	Accession of the associated protein(s) of the alpha peptide, if multiple proteins are given they should be delimited by a semicolon
Alpha Proteins Crosslink Positions	❌	int, str	13	Position of the crosslinker in the associated alpha protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Alpha Proteins Peptide Positions	❌	int, str	10	Position of the alpha peptide in the associated alpha protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Alpha Score	❌	float	0.837	Score of the alpha peptide
Alpha Decoy	❌	bool, str	False	Whether the alpha peptide is from the target (False) or decoy (True) database
Beta Peptide	✅	str	PEPKTIDE	Unmodified amino acid sequence of the beta peptide in uppercase letters
Beta Peptide Modifications	❌	str	(4:[DSS\|138.06808])	Modifications of the beta peptide, see ➡️ Modification Encoding
Beta Peptide Crosslink Position	✅	int	4	Position of the crosslinker in the beta peptide (1-based)
Beta Proteins	❌	str	G3ECR1	Accession of the associated protein(s) of the beta peptide, if multiple proteins are given they should be delimited by a semicolon
Beta Proteins Crosslink Positions	❌	int, str	13	Position of the crosslinker in the associated beta protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Beta Proteins Peptide Positions	❌	int, str	10	Position of the beta peptide in the associated beta protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Beta Score	❌	float	0.837	Score of the beta peptide
Beta Decoy	❌	bool, str	False	Whether the beta peptide is from the target (False) or decoy (True) database
CSM Score	❌	float	0.99513	Score of the crosslink-spectrum-match
Spectrum File	✅	str	2025_03_17_EXP1_RUN3_R1.raw	File name of the spectrum file
Scan Nr	✅	int	1703	The scan number of the spectrum the match was identified in
Precursor Charge	❌	int	3	Precursor charge of the crosslink spectrum
Retention Time	❌	float	530.17	Retention time of the crosslink spectrum in seconds
Ion Mobility	❌	float	170.41	Ion mobility, CCS, or compensation voltage of the crosslink spectrum

Additional resources:

Modification Encoding

Modifications are encoded with the following values:

position: The 1-based position of the modification in the peptide sequence
- should be parse-able as int data type
name: The name of the modification, for example Oxidation
- should be parse-able as str data type
mass: The monoisotopic delta mass of the modification, for example 15.994915
- should be parse-able as float data type

Any modification is then encoded as (position:[name|mass]), multiple modifications should be delimited by a semicolon ;. In the rare case that there is more than one modification on the same position, their names should be delimited by a comma ,. See examples below:

(4:[DSS|138.06808])
(1:[DSS|138.06808]);(5:[Oxidation|15.994915])
(5:[Substitution, Oxidation|13.541798])

Crosslinks

Data required for parsing crosslinks:

Column Name	Required	Data Type	Example 1	Description
Alpha Peptide	✅	str	PEPKTIDE	Unmodified amino acid sequence of the alpha peptide in uppercase letters
Alpha Peptide Crosslink Position	✅	int	4	Position of the crosslinker in the alpha peptide (1-based)
Alpha Proteins	❌	str	G3ECR1	Accession of the associated protein(s) of the alpha peptide, if multiple proteins are given they should be delimited by a semicolon
Alpha Proteins Crosslink Positions	❌	int, str	13	Position of the crosslinker in the associated alpha protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Alpha Decoy	❌	bool, str	False	Whether the alpha peptide is from the target (False) or decoy (True) database
Beta Peptide	✅	str	PEPKTIDE	Unmodified amino acid sequence of the beta peptide in uppercase letters
Beta Peptide Crosslink Position	✅	int	4	Position of the crosslinker in the beta peptide (1-based)
Beta Proteins	❌	str	G3ECR1	Accession of the associated protein(s) of the beta peptide, if multiple proteins are given they should be delimited by a semicolon
Beta Proteins Crosslink Positions	❌	int, str	13	Position of the crosslinker in the associated beta protein(s), positions in multiple proteins should be delimited by a semicolon (1-based)
Beta Decoy	❌	bool, str	False	Whether the beta peptide is from the target (False) or decoy (True) database
Crosslink Score	❌	float	0.99513	Score of the crosslink

Additional resources: