Cross-link CSV File Format
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 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
|
(b) Internally linked peptides
|
(c) Cross-linked peptides.
|
(d) Homomultimers (cross-links in which peptide sequences overlap)
|