Cross-link CSV File Format

Example files: Pol II, PP2A


Information on representing ambiguous links and different product types is below.


xiNET can display data either with or without information on the sequences of the linked peptides. The fields PepPos1, PepSeq1, PepPos2 and PepSeq2 are only used when peptide sequence information is being supplied.

COLUMN NAME
REQUIRED?
NOTES

Protein1

Yes

Identifier for protein 1

PepPos1

No

One-based residue number for peptide 1 start position in protein 1.

PepSeq1

No

Sequence for peptide 1, lowercase characters ignored.

LinkPos1

If PepSeq1 is present

One-based residue number for linkage site in peptide 1, or absolute position for link in Protein 1 if peptide position is ommitted.

Protein2

See note

Identifier for protein 2. This value is omitted for a linker modified peptide or an internally cross-linked peptide.

PepPos2

No

One-based residue number for peptide 2 start position in protein 2.

PepSeq2

No

Sequence for peptide 2, lowercase characters ignored.

LinkPos2

If PepSeq2 is present

One-based residue number for linkage site in peptide 2, or absolute position for link in Protein 2 if peptide position is ommitted.

Ommitted for linked modified peptides (mono-links).

Score

No

Confidence score – used by cut-off slider.

Id

No

Id for link

Ambiguous Linkage Sites

Ambiguous links are represented by listing the alternative linkage sites separated by commas or semi-colons in the protein and position fields. For example:

Protein1

LinkPos1

Protein2

LinkPos2

O43815; Q13033

89; 105

O43815; Q13033

96; 112

would result in these four ambiguous links being displayed:

from O43815, residue 89 to O43815, residue 96
from O43815, residue 89 to Q13033, residue 112
from Q13033, residue 105 to O43815, residue 96
from Q13033, residue 105 to Q13033, residue 112

Product types

The figures below show the representation of different product types. These are: (a) linker modified peptides; (b) internally linked peptides; and, (c) cross-linked peptides. The product type is indicated by the presence or absence of information for the second protein and second link position. We also identify a subset of cross-linked peptides, (d), in which the peptides overlap in the protein sequence.


(a) Linker modified peptides
Linker modified peptides

 

(b) Internally linked peptides
Internally linked peptides

 

(c) Cross-linked peptides.
Cross-linked peptides

 

(d) Homomultimers (cross-links in which peptide sequences overlap)
Homomultimers