(Q30397747)

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

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scholarly article

1 reference

Europe PubMed Central

16 October 2017

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

1 reference

Europe PubMed Central

16 October 2017

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1 reference

based on heuristic

inferred from title

Joshua N Adkins

6

1 reference

Europe PubMed Central

16 October 2017

Richard D. Smith

8

1 reference

Europe PubMed Central

16 October 2017

3

object named as

Nathan P Manes

1 reference

Europe PubMed Central

16 October 2017

Saiful M Chowdhury

2

object named as

Saiful M Chowdhury

1 reference

Europe PubMed Central

16 October 2017

5

object named as

M Uljana Mayer

1 reference

Europe PubMed Central

16 October 2017

author name string

Xiuxia Du

1

1 reference

Europe PubMed Central

16 October 2017

Si Wu

4

1 reference

Europe PubMed Central

16 October 2017

Gordon A Anderson

7

1 reference

Europe PubMed Central

16 October 2017

publication date

16 February 2011

1 reference

Europe PubMed Central

16 October 2017

Journal of Proteome Research

1 reference

Europe PubMed Central

16 October 2017

10

1 reference

Europe PubMed Central

16 October 2017

3

1 reference

Europe PubMed Central

16 October 2017

923-931

1 reference

Europe PubMed Central

16 October 2017

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

xComb: a cross-linked peptide database approach to protein-protein interaction analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Collision-induced dissociative chemical cross-linking reagent for protein structure characterization: applied Edman chemistry in the gas phase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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A novel approach to denoising ion trap tandem mass spectra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry

1 reference

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20 June 2018

The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes.

1 reference

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Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

1 reference

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20 June 2018

Identification of cross-linked peptides from large sequence databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers

1 reference

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20 June 2018

CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Label transfer chemistry for the characterization of protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Informatics strategies for large-scale novel cross-linking analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Performance characteristics of electron transfer dissociation mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Analysis of protein complexes using mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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An evaluation of in vitro protein-protein interaction techniques: assessing contaminating background proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Protein identification using sequential ion/ion reactions and tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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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 binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

A Universal Denoising and Peak Picking Algorithm for LC−MS Based on Matched Filtration in the Chromatographic Time Domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Chemical cross-linking and mass spectrometry for protein structural modeling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

A modular cross-linking approach for exploring protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Screening for disulfide bonds in proteins by MALDI in-source decay and LIFT-TOF/TOF-MS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Comparative assessment of large-scale data sets of protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Mapping protein-protein interactions in solution by NMR spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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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 contacts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Analysis of chromatin structure by in vivo formaldehyde cross-linking.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Specific interactions between the human RAD51 and RAD52 proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Proposal for a common nomenclature for sequence ions in mass spectra of peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

20 June 2018

Appendix 5. Nomenclature for peptide fragment ions (positive ions).

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Structural Analysis of Multiprotein Complexes by Cross-linking, Mass Spectrometry, and Database Searching

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

26 November 2018

Shotgun cross-linking analysis for studying quaternary and tertiary protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

26 November 2018

Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers.

1 reference

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Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by Fourier transform-tandem mass spectrometry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Probing three-dimensional structure of bovine serum albumin by chemical cross-linking and mass spectrometry

1 reference

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Mass spectrometric detection of affinity purified crosslinked peptides.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048902

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Characterization of an Antagonist Interleukin-6 Dimer by Stable Isotope Labeling, Cross-linking, and Mass Spectrometry

1 reference

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Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis

1 reference

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Isotope-labeled photoaffinity reagents and mass spectrometry to identify protein-ligand interactions

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https://pubmed.ncbi.nlm.nih.gov/21175198

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Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry

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https://pubmed.ncbi.nlm.nih.gov/21175198

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Identification of cross-linked peptides for protein interaction studies using mass spectrometry and 18O labeling

1 reference

https://pubmed.ncbi.nlm.nih.gov/21175198

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based on heuristic

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SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra

1 reference

https://pubmed.ncbi.nlm.nih.gov/21175198

12 December 2020

based on heuristic

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Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/21175198

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based on heuristic

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Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry

1 reference

https://pubmed.ncbi.nlm.nih.gov/21175198

12 December 2020

based on heuristic

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Identifiers

10.1021/PR100848A

1 reference

Europe PubMed Central

16 October 2017

1 reference

Europe PubMed Central

16 October 2017

1 reference

Europe PubMed Central

16 October 2017

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