(Q30891496)

27 June 2017

Building high-quality assay libraries for targeted analysis of SWATH MS data (English)

1 reference

27 June 2017

Ludovic C Gillet

2

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Olga T Schubert

Olga T Schubert

1

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George Rosenberger

George Rosenberger

5

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Ben C Collins

Ben C Collins

3

0 references

Ruedi Aebersold

11

Ruedi Aebersold

1 reference

27 June 2017

8

Dario Amodei

1 reference

27 June 2017

Pedro Navarro

4

1 reference

27 June 2017

Witold E Wolski

6

1 reference

27 June 2017

Henry Lam

7

1 reference

27 June 2017

Parag Mallick

9

1 reference

27 June 2017

Brendan MacLean

10

1 reference

27 June 2017

12 February 2015

1 reference

27 June 2017

1 reference

27 June 2017

10

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27 June 2017

426-441

1 reference

27 June 2017

3

1 reference

Options and considerations when selecting a quantitative proteomics strategy

27 June 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

mProphet: automated data processing and statistical validation for large-scale SRM experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Expansion of the ion library for mining SWATH-MS data through fractionation proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Building consensus spectral libraries for peptide identification in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Quantitative proteomic analysis of drug-induced changes in mycobacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A database of mass spectrometric assays for the yeast proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

The Mtb proteome library: A resource of assays to quantify the complete proteome of mycobacterium tuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A guided tour of the Trans-Proteomic Pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A cross-platform toolkit for mass spectrometry and proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

OpenMS - an open-source software framework for mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Development and validation of a spectral library searching method for peptide identification from MS/MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Rapid empirical discovery of optimal peptides for targeted proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Computational prediction of proteotypic peptides for quantitative proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A computational approach toward label-free protein quantification using predicted peptide detectability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

On the accuracy and limits of peptide fragmentation spectrum prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Using iRT, a normalized retention time for more targeted measurement of peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

mzML: a single, unifying data format for mass spectrometer output

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Combining results of multiple search engines in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A face in the crowd: recognizing peptides through database search

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Methods for peptide identification by spectral comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A computational tool to detect and avoid redundancy in selected reaction monitoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

File formats commonly used in mass spectrometry proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

A statistical model for identifying proteins by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

The implications of proteolytic background for shotgun proteomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

TraML--a standard format for exchange of selected reaction monitoring transition lists

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.015

31 March 2020

Identifiers

DOI

10.1038/NPROT.2015.015

1 reference

Dimensions Publication ID

27 June 2017

0 references

1 reference