Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

(2017) George Rosenberger et al.   NATURE BIOTECHNOLOGY

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes

(2016) Jennifer G. Abelin et al.   MOLECULAR & CELLULAR PROTEOMICS

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry

(2016) Robert T Lawrence et al.   NATURE METHODS

Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC–MS/MS

(2015) Aivett Bilbao et al.   JOURNAL OF PROTEOME RESEARCH

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Whole cell, label free protein quantitation with data independent acquisition: Quantitation at the MS2 level

(2014) Peter McQueen et al.   PROTEOMICS

An Untargeted Metabolomic Workflow to Improve Structural Characterization of Metabolites

(2013) Igor Nikolskiy et al.   ANALYTICAL CHEMISTRY

Phosphorylation of serine 4642 in the C-terminus of plectin by MNK2 and PKA modulates its interaction with intermediate filaments

(2013) J.-E. Bouameur et al.   JOURNAL OF CELL SCIENCE

Spectrum-based Method to Generate Good Decoy Libraries for Spectral Library Searching in Peptide Identifications

(2013) Chia-Ying Cheng et al.   JOURNAL OF PROTEOME RESEARCH

SPECTRAL DECONVOLUTION FOR GAS CHROMATOGRAPHY MASS SPECTROMETRY-BASED METABOLOMICS: CURRENT STATUS AND FUTURE PERSPECTIVES

(2013) Xiuxia Du et al.   Computational and Structural Biotechnology Journal

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry

(2009) Marshall Bern et al.   ANALYTICAL CHEMISTRY

Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics

(2009) Henry Lam et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments

(2009) Ole Schulz-Trieglaff et al.   BioData Mining

Extraction of pure components from overlapped signals in gas chromatography-mass spectrometry (GC-MS)

(2009) Vladimir A Likić   BioData Mining

Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications†

(2008) Xiuxia Du et al.   JOURNAL OF PROTEOME RESEARCH