Quantitative cross-linking/mass spectrometry

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Proteomics (156)
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pride (142)
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Technology Type

Mass Spectrometry (142)
Chemical cross-linking coupled with mass spectrometry proteomics (113)
Shotgun proteomics (39)
Affinity purification coupled with mass spectrometry proteomics (26)
Gel-based experiment (12)
Data-dependent acquisition (10)
Bottom-up proteomics (6)
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Top-down proteomics (4)
SRM/MRM (3)
SWATH MS (3)
Mass spectrometry (2)
Affinity proteomics (1)
All-ion fragmentation (1)
MSE (1)
Mass spectrometry imaging (1)

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LTQ (2)
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5975C Series GC/MSD (Agilent) (1)

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2018 (9)
2015 (4)
2011 (1)
2009 (1)
2017 (1)

CHEBI ID

CHEBI:88005 (1)
CHEBI:157728 (1)
CHEBI:3 (1)
CHEBI:157723 (1)
CHEBI:157722 (1)
CHEBI:157721 (1)
CHEBI:157720 (1)
CHEBI:157719 (1)
CHEBI:157715 (1)
CHEBI:157712 (1)
CHEBI:157711 (1)
CHEBI:157710 (1)
CHEBI:157709 (1)
CHEBI:157708 (1)
CHEBI:157707 (1)
CHEBI:157738 (1)
CHEBI:36332 (1)
CHEBI:110206 (1)
CHEBI:157737 (1)
CHEBI:10089 (1)
CHEBI:157718 (1)
CHEBI:157736 (1)
CHEBI:157735 (1)
CHEBI:1995 (1)
CHEBI:157734 (1)
CHEBI:157726 (1)
CHEBI:157733 (1)
CHEBI:157732 (1)
CHEBI:157731 (1)
CHEBI:157717 (1)

Metabolite Name

Alpha ketoglutaric acid (1)
L-2-aminoadipic acid (1)
Yangonin (1)
P-Hydroxy-7,8-dihydrokavain (1)
Dihydro-5,6-dehydrokawain (1)
Mosloflavone (1)
Kavain (1)
Prenyl caffeate (1)
Flavokawain C (1)
Flavokawain B (1)
Pipermethystine (1)
P-Hydroxykavain (1)
Methysticin (1)
Flavokawain A (1)
Dihydromethysticin (1)
Desmethoxyyangonin (1)
Cinnamalacetone (1)
((R)-3-Hydroxybutanoyl)(n-2) (1)
3,4-methylenedioxy cinnamic acid (1)
(-)-bornyl-p-coumarate (1)
(-)-bornyl-caffeate (1)
(-)-bornyl ferulate (1)
L-alpha-aminobutyric acid (1)
11-Hydroxy-12-methoxydihydrokawain (1)
Cinnamic acid (1)
10-Methoxyyangonin (1)
Lactic acid (1)
Dihydrokavain (1)
Phenylacetic acid (1)
Gamma-aminobutyric acid (1)

First Public Date

2016 (1)

Modification

2x(15)N labeled L-lysine (1)
N6 (1)

Study type

ChIP-chip by tiling array (1)
ChIP-seq (1)
Transcription profiling by array (1)

Release Date

2022 (9)
2016 (8)
2019 (8)
2025 (7)
2024 (7)
2014 (7)
2017 (6)
2015 (6)
2021 (5)
2023 (4)
2020 (4)
2018 (4)
2013 (4)
2011 (3)
2012 (3)
2026 (2)
2009 (1)

Lab affiliation

Department of Genome Sciences, University of Washington (7)
Department of Genome Sciences University of Washington USA (5)
Department of Genome Sciences, University of Washington, Seattle (4)
Functional Proteomics Lab, Faculty of Biology, University of Freiburg, Germany (3)
1. Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK 2. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Germany (2)
Department of Biology, University of Konstanz, Germany (2)
Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany (2)
Kuleuven; Department: Biologie; unit: Moleculaire Biotechnologie van Planten en Micro-organismen (2)
Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic (2)
1 Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2 Wellcome Centre for Cell Biology, School of Biologic Sciences, University of Edinburgh, Edinburgh (1)
1 Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2 Wellcome Centre for Cell Biology, School of Biologic Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom (1)
1. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; 2. Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; 3. Quantitative Biology Center (QBiC), University of Tübingen, Germany; 4. Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; 5. Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany (1)
1. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany, 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom; (1)
1. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada; 2. University of Victoria Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada; 3. Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada; 4. Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada (1)
1. University of Victoria Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada 2. Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada 3. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada 4. Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada (1)
1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 2Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 3Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China (1)
1Department of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, Minnesota 55455, USA (1)
Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK. (1)
Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany; (1)
Cambridge Centre for Proteomics, Department of Biochemistry, Gleeson Building, Tennis Court Road, Cambridge, CB21QR, United Kingdom (1)
Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK (1)
Center for Bioinformatics, Quantitative Biology Center and Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany (1)
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (1)
Centre for Proteomics and Metabolomics Head Proteomics group LUMC (1)
Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom (1)
DKFZ German Cancer Research Center Proteomics of Stem Cells and Cancer (B230) Im Neuenheimer Feld 581 69120 Heidelberg, Germany (1)
Department of Genome Sciences University of Washington (1)
Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada (1)
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark (1)
Department of Biochemistry, University of Washington, Seattle, WA, USA (1)

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On the reproducibility of label-free quantitative cross-linking/mass spectrometry

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between m...

ORGANISM(S): Homo sapiens (Human)

2018-01-02 | PXD007250 | Pride

Analysis of bilirubin-induced bovine serum albumin stability using protein denaturation and quantitative cross-linking mass spectrometry

We report the combination of protein-denaturation stability principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link rela...

ORGANISM(S): Bos taurus (Bovine)

2024-07-03 | PXD036649 | Pride

Quantitative cross-linking Protein stability Mass spectrometry

A model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers

Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue-resolution data on static proteinaceous structures. In order to investigate the technical feasibility of recording dynamic processes u...

ORGANISM(S): Homo sapiens (Human)

2016-05-06 | PXD004107 | Pride

Model dataset Isotope-labeled cross-linkers Hsa Quantitative cross-linking/mass spectromentry

Quantitative cross-linking/mass spectrometry

Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue- resolution data on static proteinaceous structures. Here we investigate the technical feasibility of recording dynamic processes usin...

ORGANISM(S): Homo sapiens (Human)

2015-06-08 | PXD002142 | Pride

Protein dynamics Structual biology Quantitation Cross-linking

Data independent acquisition cross-linking/mass spectrometry

Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independe...

ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Gallus gallus (Chicken) Equus caballus (Horse)

2019-01-25 | PXD011036 | Pride

Xi Reproducibility Spectronaut Data independent acquisition Label-free Mass spectrometry Quantitation Cross-linking

Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes

We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found ...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2016-06-16 | MSV000079827 | MassIVE

Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes

ORGANISM(S): Homo sapiens (Human)

2016-06-16 | PXD001675 | Pride

Quantitative cross-linking/mass spectrometry conformation changes human c3 activation of complement system

eXL-MS: An enhanced Cross-Linking Mass Spectrometry Workflow to Study Protein Complexes.

The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the last dec-ade. However, mostly used approaches suffer important limitations in term of efficiency and sensitivity. We describe here a new workflow based on the advanced use of the trifunction...

ORGANISM(S): Oryctolagus cuniculus (Rabbit)

2021-08-11 | PXD010422 | Pride

Creatine kinase Mass spectrometry Cross-link Monoavidin biotin affinty enrichment Click chemistry

Deciphering Mutational Effects on Inducible Nitric Oxide Synthase Conformational Dynamics via Quantitative Cross-Linking Mass Spectrometry and AlphaFold2 Subsampling

In this project, we compare the abundancies of cross-links in wild type and mutant iNOSoxyFMN-CaM complexes at specific interdomain interacting site and map the identified sites onto top AlphaFold 2 models for better understanding of iNOS protein dynamics.

ORGANISM(S): Homo sapiens (Human)

2025-10-30 | PXD064795 | Pride

Nos Targeted Cross-linking mass spectrometry

Quantitative cross-linking/mass spectrometry analysis revealed unknown structure of complement iC3

We applied quantitative cross-linking/mass spectrometry (QCLMS) to interrogate the structure of iC3 (or C3(H2O)), the activated hydrolytic product of the abundant human complement protein C3. The slow but spontaneous and ubiquitous formation of iC3 from C3 initiates antibody-independent activation o...

ORGANISM(S): Homo sapiens (Human)

2016-06-17 | PXD003486 | Pride

Quantitative cross-linking/mass spectrometry domain architecture activation of complement system alternative pathway

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