Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry

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Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry is …
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scholarly articleQ13442814

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P356DOI10.1021/PR100848A
P932PMC publication ID3048902
P698PubMed publication ID21175198
P5875ResearchGate publication ID49699526

P50authorRichard D. SmithQ7325058
Joshua N AdkinsQ38305085
Nathan ManesQ42857494
Saiful M ChowdhuryQ87883041
M Uljana MayerQ117262486
P2093author name stringXiuxia Du
Si Wu
Gordon A Anderson
P2860cites workAn approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseQ27861106
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Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contactsQ30919410
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A modular cross-linking approach for exploring protein interactionsQ31132902
MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides.Q31151456
A Universal Denoising and Peak Picking Algorithm for LC−MS Based on Matched Filtration in the Chromatographic Time DomainQ33194995
Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexesQ33215313
CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysisQ33219785
Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometryQ33225858
Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes.Q33231241
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xComb: a cross-linked peptide database approach to protein-protein interaction analysisQ33543318
Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometryQ34011047
Mapping protein-protein interactions in solution by NMR spectroscopyQ34481211
Analysis of protein complexes using mass spectrometryQ34642068
Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexesQ35616628
CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins.Q36684998
Informatics strategies for large-scale novel cross-linking analysisQ36777522
Label transfer chemistry for the characterization of protein-protein interactionsQ36862262
Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identificationsQ36915280
In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkersQ36978992
Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometryQ37113848
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Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometryQ37621068
Specific interactions between the human RAD51 and RAD52 proteinsQ38362911
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Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner bindingQ42625456
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Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfacesQ44066233
Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysisQ44868630
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Mass spectrometric detection of affinity purified crosslinked peptides.Q44897214
Probing three-dimensional structure of bovine serum albumin by chemical cross-linking and mass spectrometryQ44994470
Shotgun cross-linking analysis for studying quaternary and tertiary protein structuresQ44998283
Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by Fourier transform-tandem mass spectrometry.Q46647840
A comparison of labeling and label-free mass spectrometry-based proteomics approaches.Q47821579
Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complexQ48511507
Appendix 5. Nomenclature for peptide fragment ions (positive ions).Q50704572
Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkersQ51094319
Structural Analysis of Multiprotein Complexes by Cross-linking, Mass Spectrometry, and Database SearchingQ57898869
Characterization of an Antagonist Interleukin-6 Dimer by Stable Isotope Labeling, Cross-linking, and Mass SpectrometryQ58039486
Identification of cross-linked peptides for protein interaction studies using mass spectrometry and 18O labelingQ74799130
Isotope-labeled photoaffinity reagents and mass spectrometry to identify protein-ligand interactionsQ79432081
Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactionsQ81207959
SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectraQ82551038
Pro-CrossLink. Software tool for protein cross-linking and mass spectrometryQ83033404
Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometryQ83871420
P433issue3
P921main subjectautomationQ184199
data analysisQ1988917
P304page(s)923-931
P577publication date2011-02-16
P1433published inJournal of Proteome ResearchQ3186939
P1476titleXlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry
P478volume10

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