Crosslink or Acetyl Data Upload to XLinkDB
The tab delimited file must contain a header line with the following column names:
1. PeptideA
2. ProteinA (with optional ,nsp1,wt1,ProteinA2,nsp2,wt2,.....)
3. Cross-linkPositionA
4. PeptideB
5. ProteinB (with optional ,nsp1,wt1,ProteinB2,nsp2,wt2,.....)
6. Cross-linkPositionB
7. Confidence
Optional additional crosslink columns include:
8. NumberIDs
Additional columns for quantitation can be added with names, for each quantified sample, as:
9. Exp_Ref_Type_log2ratio
10. Exp_Ref_Type_log2stdev
11. Exp_Ref_Type_numreps
12. Exp_Ref_Type_pvalue
13. Exp_Ref_Type_chromatogram
where 'Exp', 'Ref', 'Type' are the experiment condition, reference condition, and quantitation type ('silac', 'd0/d8'), respectively.
They must in combination be unique for each included ratio. The Exp_Ref_Type_log2stdev, Exp_Ref_Type_numreps, Exp_Ref_Type_pvalue, and Exp_Ref_Type_chromatogram columns are optional.
Values stored in columns of each non-header entry of the file are:
1. First peptide sequence, without modifications
2. Protein1,nsp1,wt1,Protein2,nsp2,wt2..... where Protein1, Protein2, ... are the ranked list of protein Uniprot IDs corresponding to the first peptide,
with their numbers of sibling peptides (nsp) and weight (wt) apportioned by ProteinProphet (13), when available. Only a single Protein is required. When multiple proteins are included, each must be accompanied by its nsp and wt.
3. Position in sequence of first peptide, starting with 0 for the N-terminal residue
4. Second peptide sequence, without modifications
5. Protein1,nsp1,wt1,Protein2,nsp2,wt2..... where Protein1, Protein2, ... are the ranked list of protein Uniprot IDs corresponding to the second peptide,
with their numbers of sibling peptides (nsp) and weight (wt) apportioned by ProteinProphet, when available. Only a single Protein is required. When multiple proteins are included, each must be accompanied by its nsp and wt.
6. Position in sequence of second peptide, starting with 0 for the N-terminal residue
Additional optional columns:
7. Probability that the non-redundant crosslink is correctly identified in the data set, a value between 0 and 1
8. Number of identifications of the non-redundant crosslink in the dataset
Additional columns for quantitation:
9. Mean log2 ratio of experiment to reference condition, among contributing replicates
10. Standard deviation of log2ratios among contributing replicates
11. Number of contributing replicates (integer greater than 0)
12. P-value assessing likelihood of observing mean log2 ratio by chancev
13. Chromatogram, enabling one to view the light and heavy parent raw data traces upon clicking a log2ratio value in the table or Cytoscape colored network edge.
They must be extracted out of the raw data for the experiment and reference parent peaks ranging over the time of quantitation. As many as four chromatograms can be imported, separated by commas and written as an extended single line. The format is given below, and requires square bracket delimiters as illustrated:
[[silac,ms1_exp,m/z,Rawfilename,NormalizationFactor],
[2580.8,0],[2581.4,0],[2582.0,0],[2588.8,281176],[2589.9,195922],....., [2536.7,0]],
[[silac,ms1_ref,m/z,Rawfilename, NormalizationFactor],
[2580.8,0],[2581.4,0],[2582.0,0],[2588.8,190996],[2589.9,236953],....., [2609.6,0]]
where ms1_exp and ms1_ref indicate the extracted ms1 data for the experimental and reference conditions, respectively. One must specify m/z values of the light and heavy parent peaks,
Rawfilename, the name of the raw data file, and NormalizationFactor, the amount added to each log2ratio to center the distribution (0 when no normalization was applied). This is useful to display along with the chromatogram so researchers know how it resulted in the recorded log2ratio.
'd0/d8' can be substituted for 'silac' when appropriate. The following brackets each contain pairs of retention time in seconds, and the integrated peak intensity within ppm tolerance.
Note that the first, third, fourth, and sixth columns must be unique in the uploaded file, since they together define a unique crosslink. For the protein columns,
when ProteinProphet results are known, one can include its apportionment of the number of sibling peptides and weight to the proteins, as indicated above, following the protein Uniprot ID.
