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xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

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The encoding of cross-linking reaction product types in xiNET's CLMS-CSV file format. xiNET displays and distinguishes all three cross-linking reaction product types, these are: A, linker modified peptides; B, internally linked peptides; and, C, cross-linked peptides. The tables show the input data for the example above it. In the input data, the product type is indicated by the presence or absence of information for the second protein and second link position. xiNET also identifies a subset of cross-linked peptides, D homomultimer links, in which the peptides overlap in the protein sequence. The overlapping region is highlighted in red. The tables also include examples in which peptide sequence information is omitted—in this case the columns LinkPos1 and LinkPos2 give the absolute position of the linkage site in the protein sequence. To record ambiguous linkage sites the values in the required columns are made into comma separated lists of alternatives. Note that peptide-level ambiguity must be treated differently depending on whether the product type is an internally linked peptide, B, or cross-linked peptides, C.
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Figure 5: The encoding of cross-linking reaction product types in xiNET's CLMS-CSV file format. xiNET displays and distinguishes all three cross-linking reaction product types, these are: A, linker modified peptides; B, internally linked peptides; and, C, cross-linked peptides. The tables show the input data for the example above it. In the input data, the product type is indicated by the presence or absence of information for the second protein and second link position. xiNET also identifies a subset of cross-linked peptides, D homomultimer links, in which the peptides overlap in the protein sequence. The overlapping region is highlighted in red. The tables also include examples in which peptide sequence information is omitted—in this case the columns LinkPos1 and LinkPos2 give the absolute position of the linkage site in the protein sequence. To record ambiguous linkage sites the values in the required columns are made into comma separated lists of alternatives. Note that peptide-level ambiguity must be treated differently depending on whether the product type is an internally linked peptide, B, or cross-linked peptides, C.

Mentions: We prefer the CLMS-CSV format to the XQuest output format because CLMS-CSV stores peptide sequences and link positions within peptides as separate columns. XQuest output concatenates this information together and records it as the identifier. However, for the convenience of XQuest users, xiNET reads XQuest output directly as it is very similar to its own CLMS-CSV format. Fig. 5 describes how the different product types are recorded in CLMS-CSV, though they can also be read from XQuest output directly.


xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

The encoding of cross-linking reaction product types in xiNET's CLMS-CSV file format. xiNET displays and distinguishes all three cross-linking reaction product types, these are: A, linker modified peptides; B, internally linked peptides; and, C, cross-linked peptides. The tables show the input data for the example above it. In the input data, the product type is indicated by the presence or absence of information for the second protein and second link position. xiNET also identifies a subset of cross-linked peptides, D homomultimer links, in which the peptides overlap in the protein sequence. The overlapping region is highlighted in red. The tables also include examples in which peptide sequence information is omitted—in this case the columns LinkPos1 and LinkPos2 give the absolute position of the linkage site in the protein sequence. To record ambiguous linkage sites the values in the required columns are made into comma separated lists of alternatives. Note that peptide-level ambiguity must be treated differently depending on whether the product type is an internally linked peptide, B, or cross-linked peptides, C.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 5: The encoding of cross-linking reaction product types in xiNET's CLMS-CSV file format. xiNET displays and distinguishes all three cross-linking reaction product types, these are: A, linker modified peptides; B, internally linked peptides; and, C, cross-linked peptides. The tables show the input data for the example above it. In the input data, the product type is indicated by the presence or absence of information for the second protein and second link position. xiNET also identifies a subset of cross-linked peptides, D homomultimer links, in which the peptides overlap in the protein sequence. The overlapping region is highlighted in red. The tables also include examples in which peptide sequence information is omitted—in this case the columns LinkPos1 and LinkPos2 give the absolute position of the linkage site in the protein sequence. To record ambiguous linkage sites the values in the required columns are made into comma separated lists of alternatives. Note that peptide-level ambiguity must be treated differently depending on whether the product type is an internally linked peptide, B, or cross-linked peptides, C.
Mentions: We prefer the CLMS-CSV format to the XQuest output format because CLMS-CSV stores peptide sequences and link positions within peptides as separate columns. XQuest output concatenates this information together and records it as the identifier. However, for the convenience of XQuest users, xiNET reads XQuest output directly as it is very similar to its own CLMS-CSV format. Fig. 5 describes how the different product types are recorded in CLMS-CSV, though they can also be read from XQuest output directly.

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

Show MeSH
Related in: MedlinePlus