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Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

https://doi.org/10.1093/bioinformatics/btq054
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1017/cbo9780511530104openalex-snapshot
Purely Functional Data Structures
inferredcites →https://doi.org/10.1021/ac060279nopenalex-snapshot
Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries
inferredcites →https://doi.org/10.1021/ac701649eopenalex-snapshot
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inferredcites →https://doi.org/10.1021/pr801028bopenalex-snapshot
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inferredcites →https://doi.org/10.1038/nbt.1546openalex-snapshot
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inferredcites →https://doi.org/10.1074/mcp.m400031-mcp200openalex-snapshot
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inferredcites →https://doi.org/10.1074/mcp.m700504-mcp200openalex-snapshot
MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btn323openalex-snapshot
ProteoWizard: open source software for rapid proteomics tools development
inferredcites →https://doi.org/10.1093/nar/gkj040openalex-snapshot
The PeptideAtlas project

What points at this work

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inferred← citeshttps://doi.org/10.1002/pld3.122openalex-snapshot
Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis
inferred← citeshttps://doi.org/10.1002/pmic.201000492openalex-snapshot
Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
inferred← citeshttps://doi.org/10.1002/pmic.201000665openalex-snapshot
An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates
inferred← citeshttps://doi.org/10.1002/pmic.201000736openalex-snapshot
The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses
inferred← citeshttps://doi.org/10.1002/pmic.201100348openalex-snapshot
Proteomic analysis of the androgen receptor via MS‐compatible purification of biotinylated protein on streptavidin resin
inferred← citeshttps://doi.org/10.1002/pmic.201100387openalex-snapshot
Mass spectrometry‐based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins
inferred← citeshttps://doi.org/10.1002/pmic.201100463openalex-snapshot
Using i RT , a normalized retention time for more targeted measurement of peptides
inferred← citeshttps://doi.org/10.1002/pmic.201100482openalex-snapshot
Application of targeted proteomics to metabolically engineered E scherichia coli
inferred← citeshttps://doi.org/10.1002/pmic.201100515openalex-snapshot
PASSEL : The P eptide A tlas SRM experiment library
inferred← citeshttps://doi.org/10.1002/pmic.201100543openalex-snapshot
Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
inferred← citeshttps://doi.org/10.1002/pmic.201100566openalex-snapshot
Sigpep: Calculating unique peptide signature transition sets in a complete proteome background
inferred← citeshttps://doi.org/10.1002/pmic.201100571openalex-snapshot
An assessment of current bioinformatic solutions for analyzing LC ‐ MS data acquired by selected reaction monitoring technology
inferred← citeshttps://doi.org/10.1002/pmic.201100587openalex-snapshot
Multiplexed quantification of estrogen receptor and HER 2/ N eu in tissue and cell lysates by peptide immunoaffinity enrichment mass spectrometry
inferred← citeshttps://doi.org/10.1002/pmic.201100601openalex-snapshot
SRM targeted proteomics in search for biomarkers of HCV ‐induced progression of fibrosis to cirrhosis in HALT ‐ C patients
inferred← citeshttps://doi.org/10.1002/pmic.201200042openalex-snapshot
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
inferred← citeshttps://doi.org/10.1002/pmic.201200190openalex-snapshot
Serum proteomics in amnestic mild cognitive impairment
inferred← citeshttps://doi.org/10.1002/pmic.201200268openalex-snapshot
A guide for integration of proteomic data standards into laboratory workflows
inferred← citeshttps://doi.org/10.1002/pmic.201200298openalex-snapshot
Oncogene‐induced cellular senescence elicits an anti‐ W arburg effect
inferred← citeshttps://doi.org/10.1002/pmic.201200412openalex-snapshot
Quantitative analysis of chaperone network throughput in budding yeast
inferred← citeshttps://doi.org/10.1002/pmic.201200417openalex-snapshot
Quantitative measurements of N ‐linked glycoproteins in human plasma by SWATH ‐ MS
inferred← citeshttps://doi.org/10.1002/pmic.201300259openalex-snapshot
Exploring intercellular signaling by proteomic approaches
inferred← citeshttps://doi.org/10.1002/pmic.201300352openalex-snapshot
Exploring skyline for both MS E ‐based label‐free proteomics and HRMS quantitation of small molecules
inferred← citeshttps://doi.org/10.1002/pmic.201300402openalex-snapshot
Proteomic identification of potential prognostic biomarkers in resectable pancreatic ductal adenocarcinoma
inferred← citeshttps://doi.org/10.1002/pmic.201300551openalex-snapshot
Transcriptomics assisted proteomic analysis of N icotiana occidentalis infected by C andidatus P hytoplasma mali strain AT
inferred← citeshttps://doi.org/10.1002/pmic.201400060openalex-snapshot
Site‐specific human histone H3 methylation stability: fast K4me3 turnover
inferred← citeshttps://doi.org/10.1002/pmic.201400092openalex-snapshot
Probing phosphorylation‐dependent protein interactions within functional domains of histone deacetylase 5 ( HDAC 5)
inferred← citeshttps://doi.org/10.1002/pmic.201400232openalex-snapshot
Comprehensive identification of phosphorylation sites on the Numb endocytic adaptor protein
inferred← citeshttps://doi.org/10.1002/pmic.201400270openalex-snapshot
SWATH enables precise label‐free quantification on proteome scale
inferred← citeshttps://doi.org/10.1002/pmic.201400274openalex-snapshot
A novel targeted proteomics method for identification and relative quantitation of difference in nitration degree of OGDH between healthy and diabetic mouse
inferred← citeshttps://doi.org/10.1002/pmic.201400281openalex-snapshot
Representation of selected‐reaction monitoring data in the mzQuantML data standard
inferred← citeshttps://doi.org/10.1002/pmic.201400323openalex-snapshot
Processing strategies and software solutions for data‐independent acquisition in mass spectrometry
inferred← citeshttps://doi.org/10.1002/pmic.201400355openalex-snapshot
A mammalian transcription factor‐specific peptide repository for targeted proteomics
inferred← citeshttps://doi.org/10.1002/pmic.201400364openalex-snapshot
LC‐MS/MS‐based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma
inferred← citeshttps://doi.org/10.1002/pmic.201400373openalex-snapshot
Tools for monitoring system suitability in LC MS/MS centric proteomic experiments
inferred← citeshttps://doi.org/10.1002/pmic.201400396openalex-snapshot
In‐depth evaluation of software tools for data‐independent acquisition based label‐free quantification
inferred← citeshttps://doi.org/10.1002/pmic.201400412openalex-snapshot
Viewing the proteome: How to visualize proteomics data?
inferred← citeshttps://doi.org/10.1002/pmic.201400416openalex-snapshot
Allergen relative abundance in several wheat varieties as revealed via a targeted quantitative approach using MS
inferred← citeshttps://doi.org/10.1002/pmic.201400450openalex-snapshot
Advances in high‐resolution accurate mass spectrometry application to targeted proteomics
inferred← citeshttps://doi.org/10.1002/pmic.201400466openalex-snapshot
Studying macromolecular complex stoichiometries by peptide‐based mass spectrometry
inferred← citeshttps://doi.org/10.1002/pmic.201400594openalex-snapshot
Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection
inferred← citeshttps://doi.org/10.1002/pmic.201500048openalex-snapshot
Enhancing bottom‐up and top‐down proteomic measurements with ion mobility separations
inferred← citeshttps://doi.org/10.1002/pmic.201500058openalex-snapshot
The use of ubiquitin lysine mutants to characterize E2–E3 linkage specificity: Mass spectrometry offers a cautionary “tail”
inferred← citeshttps://doi.org/10.1002/pmic.201500224openalex-snapshot
A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva
inferred← citeshttps://doi.org/10.1002/pmic.201500449openalex-snapshot
Advances in targeted proteomics and applications to biomedical research
inferred← citeshttps://doi.org/10.1002/pmic.201500450openalex-snapshot
Application of wide selected‐ion monitoring data‐independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor
inferred← citeshttps://doi.org/10.1002/pmic.201500453openalex-snapshot
Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non‐small cell lung cancer
inferred← citeshttps://doi.org/10.1002/pmic.201500482openalex-snapshot
Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label‐free proteomics approaches
inferred← citeshttps://doi.org/10.1002/pmic.201500488openalex-snapshot
High‐precision iRT prediction in the targeted analysis of data‐independent acquisition and its impact on identification and quantitation
inferred← citeshttps://doi.org/10.1002/pmic.201500492openalex-snapshot
Multi‐mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra
inferred← citeshttps://doi.org/10.1002/pmic.201500500openalex-snapshot
Advances in quadrupole and time‐of‐flight mass spectrometry for peptide MRM based translational research analysis
inferred← citeshttps://doi.org/10.1002/pmic.201500502openalex-snapshot
Targeted proteomics coming of age – SRM, PRM and DIA performance evaluated from a core facility perspective
inferred← citeshttps://doi.org/10.1002/pmic.201500503openalex-snapshot
Absolute protein quantification of the yeast chaperome under conditions of heat shock
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