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Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

https://doi.org/10.1101/424697
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Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/pro.2458openalex-snapshot
Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances
inferredcites →https://doi.org/10.1016/j.jprot.2016.10.014openalex-snapshot
A multicentric study to evaluate the use of relative retention times in targeted proteomics
inferredcites →https://doi.org/10.1016/j.str.2018.03.011openalex-snapshot
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules
inferredcites →https://doi.org/10.1021/ac0488762openalex-snapshot
Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein−Protein Interactions
inferredcites →https://doi.org/10.1021/ac991081oopenalex-snapshot
A Generic Strategy To Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry
inferredcites →https://doi.org/10.1021/acs.jproteome.7b00370openalex-snapshot
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
inferredcites →https://doi.org/10.1021/bi010259+openalex-snapshot
Mapping Protein Interfaces with a Fluorogenic Cross-Linker and Mass Spectrometry: Application to Nebulin−Calmodulin Complexes
inferredcites →https://doi.org/10.1038/nbt.1546openalex-snapshot
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
inferredcites →https://doi.org/10.1038/nbt.3685openalex-snapshot
A multicenter study benchmarks software tools for label-free proteome quantification
inferredcites →https://doi.org/10.1038/nbt1329openalex-snapshot
The minimum information about a proteomics experiment (MIAPE)
inferredcites →https://doi.org/10.1038/ncomms15473openalex-snapshot
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
inferredcites →https://doi.org/10.1038/nmeth.1333openalex-snapshot
A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
inferredcites →https://doi.org/10.1038/nmeth.2763openalex-snapshot
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins
inferredcites →https://doi.org/10.1038/nprot.2013.168openalex-snapshot
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline
inferredcites →https://doi.org/10.1038/nprot.2014.144openalex-snapshot
A comparative cross-linking strategy to probe conformational changes in protein complexes
inferredcites →https://doi.org/10.1038/nprot.2017.113openalex-snapshot
Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins
inferredcites →https://doi.org/10.1038/nprot.2017.146openalex-snapshot
Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data
inferredcites →https://doi.org/10.1038/s41467-017-00249-5openalex-snapshot
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
inferredcites →https://doi.org/10.1073/pnas.090099097openalex-snapshot
High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry
inferredcites →https://doi.org/10.1074/mcp.m114.047050openalex-snapshot
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma
inferredcites →https://doi.org/10.1074/mcp.m117.068429openalex-snapshot
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
inferredcites →https://doi.org/10.1074/mcp.r110.000133openalex-snapshot
mzML—a Community Standard for Mass Spectrometry Data
inferredcites →https://doi.org/10.1093/nar/gkv1145openalex-snapshot
2016 update of the PRIDE database and its related tools
inferredcites →https://doi.org/10.1093/nar/gkw936openalex-snapshot
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
inferredcites →https://doi.org/10.1110/ps.9.8.1503openalex-snapshot
Chemical cross‐linking with thiol‐cleavable reagents combined with differential mass spectrometric peptide mapping—A novel approach to assess intermolecular protein contacts

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/rcm.9308openalex-snapshot
Evaluation of acquisition modes for semi‐quantitative analysis by targeted and untargeted mass spectrometry
inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00947openalex-snapshot
Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents
inferred← citeshttps://doi.org/10.1101/561829openalex-snapshot
xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data
inferred← citeshttps://doi.org/10.1515/hsz-2018-0443openalex-snapshot
Mass spectrometry of membrane protein complexes
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