(Q38748537)

1 July 2019

title

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation (English)

1 reference

1 July 2019

1 reference

1 reference

Tomi Suomi

2

0 references

Laura L. Elo

object named as

Laura L Elo

series ordinal

3

0 references

author name string

Tommi Välikangas

series ordinal

1

1 reference

1 July 2019

publication date

1 November 2018

1 reference

1 July 2019

Briefings in Bioinformatics

published in

1 reference

1 July 2019

volume

19

1 reference

1 July 2019

issue

6

1 reference

1 July 2019

page(s)

1344-1355

1 reference

1 July 2019

Label-free quantification in clinical proteomics

cites work

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Options and considerations when selecting a quantitative proteomics strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Multiplexed MS/MS for improved data-independent acquisition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Data processing methods and quality control strategies for label-free LC-MS protein quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

LC-MS alignment in theory and practice: a comprehensive algorithmic review

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Generic workflow for quality assessment of quantitative label-free LC-MS analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Review of peak detection algorithms in liquid-chromatography-mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Normalization and missing value imputation for label-free LC-MS analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Missing value imputation improves clustering and interpretation of gene expression microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Optimization of Statistical Methods Impact on Quantitative Proteomics Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

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/10.1093%2FBIB%2FBBX054

Andromeda: a peptide search engine integrated into the MaxQuant environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

TANDEM: matching proteins with tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

MS-GF+ makes progress towards a universal database search tool for proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Dinosaur: A Refined Open-Source Peptide MS Feature Detector

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

OpenMS - an open-source software framework for mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

A Bayesian missing value estimation method for gene expression profile data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

pcaMethods--a bioconductor package providing PCA methods for incomplete data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Missing value imputation for microarray gene expression data using histone acetylation information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Missing value estimation for DNA microarray gene expression data: local least squares imputation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Improving missing value estimation in microarray data with gene ontology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Missing value estimation methods for DNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Reproducibility-optimized test statistic for ranking genes in microarray studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

pROC: an open-source package for R and S+ to analyze and compare ROC curves

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Detecting Significant Changes in Protein Abundance

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

DNA microarray data imputation and significance analysis of differential expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX054

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Mass spectrometry-based label-free quantitative proteomics

1 reference

12 December 2020

A systematic evaluation of normalization methods in quantitative label-free proteomics

1 reference

12 December 2020

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

1 reference

12 December 2020

Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology

1 reference

12 December 2020

Identifiers

DOI

10.1093/BIB/BBX054

1 reference

1 July 2019

journals/bib/ValikangasSE18a

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 July 2019

PubMed publication ID

28575146

1 reference

1 July 2019