MassIVE MSV000080758

Imported Reanalysis Dataset Public PXD003880

Xilmass: a new approach towards the identification of cross-linked peptides

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Description

Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in a novel way in the search database that explicitly encodes cross-linking sites and (ii) the scoring function from the Andromeda algorithm was adapted to score against a theoretical MS spectrum that contains the peaks from all the possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was subsequently evaluated against the recently published Kojak and the popular pLink algorithms on a data set that contains calmodulin-plectin. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: human ; calmodulin ; the actin-binding domain (ABD) of plectin ; cross-linking ; DSS

Contact

Principal Investigators:
(in alphabetical order) 		Lennart Martens, Group Leader, N/A
Submitting User: ccms

Publications

Y?lmaz ?, Drepper F, Hulstaert N, ?erni? M, Gevaert K, Economou A, Warscheid B, Martens L, Vandermarliere E.
Xilmass: A New Approach toward the Identification of Cross-Linked Peptides.
Anal. Chem. 2016 Oct 18;88(20):9949-9957. Epub 2016 Sep 28.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.