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ProteomicsOptimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples
Data independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be ...
ORGANISM(S): Candida albicans (Yeast) Mus musculus (Mouse) 
2023-10-11 | PXD045958 | Pride
Data quality Spectronaut False positives Immunology C. albicans Mouse Infection Dia Xic Multi-species 
UnknownSpectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.
Not available
S-EPMC12903166 | biostudies-literature
UnknownSpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.
Not available
S-EPMC11893148 | biostudies-literature
UnknownOptimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples.
Not available
S-EPMC11165578 | biostudies-literature
ProteomicsSingle cell proteomics of human brain neutrophils from glioblastoma patients
FACS sorted single cell proteomes of glioblastoma derived neutrophils. Brain tissue was dissociated and individual neutrophils were FACS sorted into 384 well plates into master mix containing. The cells were later processed on the CellenOne and analysed on an Orbitrap Astral with FAIMS Pro. The data...
ORGANISM(S): Homo sapiens (Human) 
2025-11-18 | PXD061065 | Pride
Glioblastoma Scp Single cell Gbm Astral Brain Neutrophils Spectronaut 
ProteomicsData 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 
ProteomicsInefficient secretion of anti-sigma factor FlgM inhibits bacterial motility at high temperature
Regulation of gene expression according to the environmental conditions is vitally important for all living organisms. Temperature is one of the key cues for microorganisms that can exist in different environments, and several mechanisms of temperature-dependent re-allocation of cellular resources h...
ORGANISM(S): Escherichia coli 
2019-08-14 | PXD012611 | Pride
Motolity Data-independent acquisition E.coli 
ProteomicsDIA Quantification Proteomics of rat tissues including bph and sham rats
In this project, Q-Exactive HF(Thermo Fisher Scientific,San Jose,CA) was used to acquire mass spectrometry (MS) data for 7 samples in Data Independent Acquisition (DIA) mode. Quantification of peptides and proteins was performed using Spectronaut™ and MSstats software packages
ORGANISM(S): Rattus norvegicus (Rat) 
2025-12-01 | PXD032395 | Pride
Lc-msms Prostate Rats 
ProteomicsProteomic and Machine Learning Analyses Reveal the Mechanism of Baicalin in Inhibiting Biofilm Formation of Escherichia coli
This study investigated the proteomic profiles of Escherichia coli under different MBIC treatment levels using data-independent acquisition (DIA) quantitative proteomics. The dataset included five experimental groups (A-E), with four biological replicates per group, resulting in a total of 20 biolog...
ORGANISM(S): Escherichia coli 
2026-09-08 | PXD083748 | Pride
Dia Spectronaut Escherichia coli Astral Mbic Quantitative proteomics Lc-ms/ms 
ProteomicsCalculating coefficients of variation for data independent acquisition-based proteomics
Reanalysis of the Kawashima et al dataset with DIA-NN and Spectronaut. By using different settings this shows how the CVs can be altered by the software parameters.
ORGANISM(S): Homo sapiens (Human) 
2024-05-20 | PXD052403 | Pride
Intensity Proteomics Cv Coefficient of variation 
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