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ProteomicsRobust and easy-to-use one pot workflow for label free single cell proteomics
The analysis of ultra-low input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here we report a comprehensive workflow that includes optimized strategies for all ste...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-01-26 | MSV000091156 | MassIVE
ProteomicsMS Annika: A new Cross-Linking Search Engine
A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2021-05-27 | PXD022772 | Pride
Xl-ms Proteome-discoverer Ion-mobility Search-engine 
ProteomicsLabel-Free Single Cell Proteomics Utilizing Ultrafast LC and MS Instrumentation: A Valuable Complementary Technique to Multiplexing.
In recent years, single cell proteomics became one of the hottest topics within the field of proteomics. The potential ability to map the proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotypes and cellular functions. In co...
ORGANISM(S): Homo sapiens (Human) 
2023-02-09 | PXD039208 | Pride
Dia Label-free-proteomics Data-completness Dda 
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 
ProteomicsIn vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome.
Cross-linking mass spectrometry has evolved as a powerful technique to study protein-protein interactions and to provide structural information over the past decades. Low reaction efficiencies, and complex matrices lead to challenging system wide crosslink analysis. In this study, we improved and st...
ORGANISM(S): Homo sapiens (Human) 
2025-08-21 | PXD061173 | Pride
Affinity enrichment Ddx39b Xl-ms Dsbso 
ProteomicsFast and highly efficient affinity enrichment of Azide-A-DSBSO cross-linked peptides.
Cross-linking mass spectrometry is an increasingly used, powerful technique to study protein-protein interactions or to provide structural information. Due to sub-stochiometric reaction efficiencies, cross-linked peptides are usually low abundant. This results in challenging data evaluation and the ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2020-05-11 | PXD016963 | Pride
Click reaction Affinity enrichment Cross-linking Mass spectrometry Dbco Dsbso 
ProteomicsXL-MS data analysis with MeroX and XlinkX
Comparison of MeroX in different modes and XlinkX upon variation of database size based on DSBU linked BSA as test-dataset
ORGANISM(S): Bos taurus (Bovine) 
2020-11-17 | PXD021648 | Pride
Mass-spectromerty Dsbu Xlinkx Merox Crosslinking Bsa 
ProteomicsA molecular network of conserved factors keeps ribosomes dormant in the egg
Ribosomes are produced in large quantities during oogenesis and stored in the egg. However, the egg and early embryo are translationally inactive. How translation is activated during embryogenesis is poorly understood. Using mass-spectrometry and cryo-EM analyses of ribosomes isolated from zebrafish...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) Xenopus laevis (African clawed frog) 
2022-11-03 | PXD026866 | Pride
Cryo-em Cross-linking Xenopus Mass-spectrometry Ribosome Zebrafish 
ProteomicsChallenging the Astral mass analyzer – up to 5300 proteins per single-cell at unseen quantitative accuracy to study cellular heterogeneity.
This is an additional dataset to PXD049412 A detailed proteome map is crucial for understanding molecular pathways and protein functions. Despite significant advancements in sample preparation, instrumentation, and data analysis, single-cell proteomics is currently limited by proteomic depth and qua...
ORGANISM(S): Homo sapiens (Human) 
2025-06-03 | PXD064564 | Pride
Mass spectrometry Astral A549 Liquid chromatography Aurora column Single-cell proteomics Trophectoderm-like cells Naïve human stem cells 
ProteomicsLow-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics
Field Asymmetric Ion Mobility Spectrometry (FAIMS) is an indispensable tool in single-cell and low-input proteomics. Here, we show that tuning FAIMS resolution via electrode temperature modulation improves sensitivity. We demonstrate that lowering FAIMS resolution broadens the compensation voltage w...
ORGANISM(S): Homo sapiens (Human) 
2026-04-14 | PXD069335 | Pride
Low-input proteomics Ion mobility filter Single cell proteomics Faims 
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