SDRF template for crosslinking mass spectrometry (XL-MS) experiments. Extends ms-proteomics with crosslinking-specific columns for data analysis.
The crosslinking template adds XL-MS-specific columns for structural proteomics studies.
Cross-linker identity is required and enrichment is recommended for proper data interpretation.
Key guidance:
comment[cross-linker]: Required. Use structured format with ontology accession:NT=DSS;AC=XLMOD:02001 for simple notation, or extended format with cleavability,
target residues, and mass: NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98.
characteristics[enrichment process]: Recommended. Should be enrichment of cross-linked peptides.comment[dissociation method]: Required (overridden from ms-proteomics recommended).Dissociation method critically affects cleavable linker stub ion generation.
Common: HCD, CID, ETD, EThcD, stepped HCD.
comment[collision energy]: Recommended. Stepped collision energies are common forcleavable linkers (e.g., 25 NCE;27 NCE;30 NCE).
characteristics[crosslink distance]: Maximum Calpha-Calpha distance constraint inAngstroms (30 Å for DSS/BS3, 26.4 Å for DSSO, 11.4 Å for EDC zero-length).
comment[crosslinker to protein ratio]: Molar ratio (50:1, 100:1).Common cross-linkers: DSS (XLMOD:02001), BS3 (XLMOD:02000), DSSO (XLMOD:02010, cleavable),
EDC (XLMOD:02009, zero-length).
| Column | Requirement | Source | Description | |
|---|---|---|---|---|
| comment[dissociation method] | required | crosslinking | Fragmentation method used in MS2. Critical for cleavable crosslinkers (DSSO, DSBU) which generate... | |
|
Fragmentation method used in MS2. Critical for cleavable crosslinkers (DSSO, DSBU)
which generate diagnostic stub ions under specific fragmentation conditions.
ontology
— ontologies: ms, pride
Dissociation method should be a child term of MS:1000044
HCD, CID, ETD, EThcD, stepped HCD
|
||||
| comment[cross-linker] | required | crosslinking | Cross-linker compound with structured properties for analysis tools. Format: NT=name;AC=accession... | |
|
Cross-linker compound with structured properties for analysis tools.
Format: NT=name;AC=accession;CL=cleavable;TA=targets;MH/ML=stub masses
Uses XLMOD ontology (parent term XLMOD:00004).
structured_kv
Cross-linker in ontology format: NT=name;AC=ontology:accession
NT=DSS;AC=XLMOD:02001, NT=BS3;AC=XLMOD:02000, NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98, NT=EDC;AC=XLMOD:02009;CL=no;TA=K,D,E
|
||||
| characteristics[enrichment process] | recommended | crosslinking | Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide e... | |
|
Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment)
ontology
— ontologies: pride, efo
Enrichment type should be a child term of EFO:0009090 (enrichment process)
enrichment of cross-linked peptides, enrichment of phosphorylated protein, enrichment of glycopeptides, enrichment of ubiquitinated proteins
|
||||
| comment[collision energy] | recommended | crosslinking | Collision energy used for fragmentation. Important for cleavable crosslinker analysis. | |
|
Collision energy used for fragmentation. Important for cleavable crosslinker analysis.
pattern
— pattern:
^\d+(\.\d+)?%?\s*(NCE|eV)(;\d+(\.\d+)?%?\s*(NCE|eV))*$|^stepped\s+.+$
Collision energy format: {value} {unit} where unit is NCE or eV. For stepped collision energies, use semicolon-separated values or 'stepped' prefix.
30 NCE, 30% NCE, 27 eV, 25 NCE;27 NCE;30 NCE, 25% NCE;27% NCE;30% NCE, stepped 27+-6%
|
||||
| comment[chemical cross-linking coupled with ms] | recommended | crosslinking | MS-based cross-linking methodology used to identify this as a crosslinking dataset | |
|
MS-based cross-linking methodology used to identify this as a crosslinking dataset
values
— values:
cross-linking mass spectrometry
Cross-linking MS methodology
|
||||
| comment[crosslink enrichment method] | recommended | crosslinking | Method used to enrich crosslinked peptides before MS analysis | |
|
Method used to enrich crosslinked peptides before MS analysis
ontology
— ontologies: pride, ms
Enrichment method (PRIDE:0000586)
size exclusion chromatography, strong cation exchange chromatography, high-pH reversed-phase chromatography, FAIMS
|
||||
| characteristics[crosslink distance] | optional | crosslinking | Maximum Cα-Cα distance constraint provided by the crosslinker (for structural interpretation) | |
|
Maximum Cα-Cα distance constraint provided by the crosslinker (for structural interpretation)
number_with_unit
Distance should be a number followed by Å (Angstrom)
30 Å, 26.4 Å, 11.4 Å
|
||||
| comment[crosslinker concentration] | optional | crosslinking | Concentration of crosslinking reagent used | |
|
Concentration of crosslinking reagent used
number_with_unit
Concentration with unit
2 mM, 500 uM, 1 mM
|
||||
| characteristics[crosslinking reaction time] | optional | crosslinking | Duration of the crosslinking reaction | |
|
Duration of the crosslinking reaction
number_with_unit
Time should be a number followed by unit
30 min, 1 h, 45 min
|
||||
| characteristics[crosslinking temperature] | optional | crosslinking | Temperature at which crosslinking was performed | |
|
Temperature at which crosslinking was performed
number_with_unit
Temperature should be a number followed by °C (e.g., 25°C or 25 °C)
25°C, 4°C, 37°C, room temperature
|
||||
| comment[crosslinker to protein ratio] | optional | crosslinking | Molar ratio of crosslinker to protein | |
|
Molar ratio of crosslinker to protein
pattern
— pattern:
^\d+:\d+(\s+\w+/\w+)?$
Ratio format (e.g., 50:1 or 1:1 w/w)
3001, 6001, 1:1 w/w
|
||||
| comment[quenching reagent] | optional | crosslinking | Reagent used to quench the crosslinking reaction | |
|
Reagent used to quench the crosslinking reaction
pattern
— pattern:
^.+$
Chemical name of quenching reagent
Tris-HCl, ammonium bicarbonate, glycine
|
||||