DIANA--algorithmic improvements for analysis of data-independent acquisition MS data

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DIANA--algorithmic improvements for analysis of data-independent acquisition MS data is …
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scholarly articleQ13442814

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P8978DBLP publication IDjournals/bioinformatics/TelemanRRSMML15
P356DOI10.1093/BIOINFORMATICS/BTU686
P698PubMed publication ID25348213

P50authorLars MalmströmQ30347545
George RosenbergerQ39404611
Hannes L. RöstQ39404671
Fredrik LevanderQ52418410
Johan MalmströmQ57009792
P2093author name stringUwe Schmitt
Johan Teleman
P2860cites workA cross-platform toolkit for mass spectrometry and proteomicsQ24629036
The PeptideAtlas projectQ25257813
mzML--a community standard for mass spectrometry dataQ28743778
Combining dependent P-valuesQ29540849
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometryQ29547311
A model for random sampling and estimation of relative protein abundance in shotgun proteomicsQ29547316
Multiplexed MS/MS for improved data-independent acquisitionQ30651066
Intelligent data acquisition blends targeted and discovery methodsQ30773676
Shotgun collision-induced dissociation of peptides using a time of flight mass analyzerQ30779818
Numerical compression schemes for proteomics mass spectrometry dataQ30787624
UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidationQ33245836
The proteios software environment: an extensible multiuser platform for management and analysis of proteomics dataQ33428180
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometryQ33639352
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomicsQ33674206
mProphet: automated data processing and statistical validation for large-scale SRM experimentsQ33851184
The global burden of group A streptococcal diseasesQ33991045
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimatesQ34005153
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysisQ34133645
PASSEL: the PeptideAtlas SRMexperiment libraryQ34154235
Protein expression changes in ovarian cancer during the transition from benign to malignantQ34218384
Automated selected reaction monitoring software for accurate label-free protein quantificationQ34289600
Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean.Q34910930
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 systemQ35026886
Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomicsQ35668824
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networksQ35749545
Accurate peptide fragment mass analysis: multiplexed peptide identification and quantificationQ35869157
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenesQ36503352
Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantificationQ36713554
Assigning significance to peptides identified by tandem mass spectrometry using decoy databasesQ37027478
Combining results of multiple search engines in proteomicsQ37160902
A database of mass spectrometric assays for the yeast proteomeQ37406219
TraML--a standard format for exchange of selected reaction monitoring transition listsQ38479687
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search enginesQ41822004
Using iRT, a normalized retention time for more targeted measurement of peptidesQ41938071
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS dataQ48317444
A direct approach to false discovery ratesQ56622258
Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide IdentificationQ57011814
P433issue4
P407language of work or nameEnglishQ1860
P304page(s)555-562
P577publication date2014-10-27
P1433published inBioinformaticsQ4914910
P1476titleDIANA--algorithmic improvements for analysis of data-independent acquisition MS data
P478volume31

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cites work (P2860)
Q61812883Q61812883
Q91085167A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs
Q89575750A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
Q112283952A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
Q64969737A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.
Q28066912Advances in targeted proteomics and applications to biomedical research
Q101053027Application of SWATH mass spectrometry in the identification of circulating proteins does not predict future weight gain in early psychosis
Q31161210Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms
Q112301185Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
Q92665025Bioinformatics approaches for improving seminal plasma proteome analysis
Q63493260Chapter 10. Data Analysis for Data Independent Acquisition
Q64966563Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.
Q61448976Complex-centric proteome profiling by SEC-SWATH-MS
Q97636489Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes
Q91452714DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
Q114867182DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
Q91801548Data-Independent Acquisition Mass Spectrometry-based Proteomics and Software Tools: A Glimpse in 2020
Q58787412Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial
Q38380171Dinosaur: A Refined Open-Source Peptide MS Feature Detector
Q35581032Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
Q38654893Enhanced differential expression statistics for data-independent acquisition proteomics
Q112288329Extending the Proteomic Characterization of Candida albicans Exposed to Stress and Apoptotic Inducers through Data-Independent Acquisition Mass Spectrometry
Q36344553Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification.
Q30982025Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry
Q29994570Identification of small molecules using accurate mass MS/MS search
Q93137971Identification of two abundant Aerococcus urinae cell wall-anchored proteins
Q36374655Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics
Q36399003Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.
Q34507442Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics
Q125343283Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization
Q38615341Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Q31150191Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry
Q88487488Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way
Q38743141Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine
Q40528229Quantitative proteogenomics of human pathogens using DIA-MS.
Q38609416Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry
Q30998330Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.
Q92936221Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Q91172986Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition
Q31018998Reproducible quantitative proteotype data matrices for systems biology
Q112291812Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach
Q104492495SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles
Q31070927SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools
Q38616270Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
Q98177089Strategies to enable large-scale proteomics for reproducible research
Q51149326Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.
Q39560421Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization
Q37225838TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
Q92468794The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers
Q112641636The impact of genomic variation on protein phosphorylation states and regulatory networks
Q104609658The role of Data-Independent Acquisition for Glycoproteomics
Q91601739The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination

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