(Q37225838)

19 August 2017

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics (English)

1 reference

19 August 2017

0 references

1 reference

10

1 reference

19 August 2017

11

Ruedi Aebersold

1 reference

19 August 2017

Matteo Zanella

4

0 references

Giuseppe D'Agostino

Giuseppe D'Agostino

3

0 references

Pedro Navarro

Pedro Navarro

5

0 references

George Rosenberger

George Rosenberger

6

0 references

Hannes L. Röst

Hannes L Röst

1

0 references

Ben C Collins

Ben C Collins

7

0 references

Yansheng Liu

Yansheng Liu

2

0 references

Giuseppe Testa

9

Giuseppe Testa

1 reference

19 August 2017

Ludovic Gillet

8

1 reference

19 August 2017

1 August 2016

1 reference

19 August 2017

1 reference

19 August 2017

13

1 reference

19 August 2017

777-783

1 reference

19 August 2017

9

1 reference

https://scigraph.springernature.com/pub.10.1038/nmeth.3954

19 August 2017

0 references

cites work

Reproducible quantitative proteotype data matrices for systems biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Prediction of colorectal cancer diagnosis based on circulating plasma proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Non-invasive prognostic protein biomarker signatures associated with colorectal cancer

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Quantitative variability of 342 plasma proteins in a human twin population

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Differential diagnosis of azoospermia with proteomic biomarkers ECM1 and TEX101 quantified in seminal plasma

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

The one hour yeast proteome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

A blood-based proteomic classifier for the molecular characterization of pulmonary nodules.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Signatures of mutational processes in human cancer

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Automated selected reaction monitoring software for accurate label-free protein quantification

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

The quantitative proteome of a human cell line.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Deep proteome and transcriptome mapping of a human cancer cell line

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Global quantification of mammalian gene expression control

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

International network of cancer genome projects

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

MaRiMba: a software application for spectral library-based MRM transition list assembly

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

ProteoWizard: open source software for rapid proteomics tools development

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

OpenMS - an open-source software framework for mass spectrometry

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

TOPP--the OpenMS proteomics pipeline

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Narrative review: protein degradation and human diseases: the ubiquitin connection

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

14 September 2017

The PeptideAtlas project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Complement factor H variant increases the risk of age-related macular degeneration

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Open mass spectrometry search algorithm

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

TANDEM: matching proteins with tandem mass spectra

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Dynamics of protein turnover, a missing dimension in proteomics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Signal maps for mass spectrometry-based comparative proteomics.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5008461

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27479329

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.3954

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.3954

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

PMCID

5008461