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ProteomicsA synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines
We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library wer...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2020-07-28 | PXD014337 | Pride
Crosslinking mass spectrometry peptide library 
UnknownA synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes.
Not available
S-EPMC7005041 | biostudies-literature
ProteomicsQuantitative photo-crosslinking mass spectrometry reveals protein structure response to environmental changes
Conformational changes of protein structures depend on their chemical and physical environment. Studying conformational changes depending on environmental parameters is notoriously difficult as many methods of structural biology are affected by parameters like temperature or pH. To make such conform...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2019-07-01 | PXD012939 | Pride
Data-independent acquisition Structural dynamics Human serum albumin Dia-qclms Quantitation Xi Cytochrome c Spectronaut Label-free Mass spectrometry Photo-crosslinking Cross-linking Sda 
ProteomicsMimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows
The field of cross-linking mass spectrometry has matured to a frequently used tool for the investiga-tion of protein structures as well as interactome studies up to a system wide level. The growing com-munity generated a broad spectrum of applications, linker types, acquisition strategies and specia...
ORGANISM(S): Escherichia coli 
2022-05-24 | PXD029252 | Pride
Mass spectrometry Ribosome Fdr Crosslinking 
UnknownMimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.
Not available
S-EPMC9270371 | biostudies-literature
ProteomicsReanalysis of a synthetic cross-linked peptide library with MaxLynx
Reanalysis of a synthetic crosslinked peptide library datasets with DSS (non-cleavable), DSSO and DSBU (MS-cleavable) cross linkers from Beveridge et al., Nat. Commun., 2020 (PXD014337)
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2022-01-11 | PXD027159 | Pride
Crosslinking 
ProteomicsGlobal Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility du...
ORGANISM(S): Homo sapiens (Human) 
2022-03-01 | PXD002929 | Pride
Crosslinking Protein-protein interactions 
TranscriptomicsFunctional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms
We characterized the functions of the understudied LUC7-like family of splicing factors in human cells using seCLIP-seq, RBP knockdown followed by RNA-seq, and Co-IP mass spectrometry.
ORGANISM(S): Homo sapiens 
2021-04-14 | E-MTAB-9709 | biostudies-arrayexpress
ProteomicsIn planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
Mass spectrometry analysis in combination with the site-specific chemical cross-linking has emerged as a powerful method in study of three-dimensional structure of protein complex and in mapping of protein-protein interactions (PPIs). Even though in vitro cross-linking experiments have been widely a...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2016-06-28 | PXD003658 | Pride
Arabidopsis Mass spectrometry Disuccinimidyl suberate In planta chemical cross-linking Interactomics Exhaustive cross-linked peptides identification tool 
GenomicsGenome-wide profile of the SWI/SNF chromatin remodeling complex
A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes includ...
ORGANISM(S): Homo sapiens 
2011-01-10 | E-GEOD-24397 | biostudies-arrayexpress
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