(Q30601945)

14 November 2017

Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies (English)

1 reference

14 November 2017

4

Kenneth Williams

1 reference

14 November 2017

Can Bruce

1

1 reference

PMCID

3688054

14 November 2017

Kathryn Stone

series ordinal

2

1 reference

PMCID

3688054

14 November 2017

Erol Gulcicek

series ordinal

3

1 reference

14 November 2017

1 March 2013

1 reference

Current Protocols in Bioinformatics

14 November 2017

1 reference

14 November 2017

Chapter 13

1 reference

14 November 2017

Unit 13.21

1 reference

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

14 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Inference and validation of protein identifications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Generic comparison of protein inference engines

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Rapid empirical discovery of optimal peptides for targeted proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Predicting protein kinase specificity: Predikin update and performance in the DREAM4 challenge

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Andromeda: a peptide search engine integrated into the MaxQuant environment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Phospho.ELM: a database of phosphorylation sites--update 2011

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Confident phosphorylation site localization using the Mascot Delta Score

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Role of spectral counting in quantitative proteomics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

20 June 2018

The PeptideAtlas Project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Trans-proteomic pipeline: a pipeline for proteomic analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

De novo sequencing methods in proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Target-decoy search strategy for mass spectrometry-based proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Mass spectrometry-based label-free quantitative proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

The Proteomics Identifications database: 2010 update

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

False discovery rates of protein identifications: a strike against the two-peptide rule

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Proteome coverage prediction with infinite Markov models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Proteomics by mass spectrometry: approaches, advances, and applications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Predicting intensity ranks of peptide fragment ions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

PhosphoPep--a database of protein phosphorylation sites in model organisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A database of mass spectrometric assays for the yeast proteome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Selected reaction monitoring for quantitative proteomics: a tutorial

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Precision proteomics: the case for high resolution and high mass accuracy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Linear Motif Atlas for Phosphorylation-Dependent Signaling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Detection of co-eluted peptides using database search methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

PhosphoScore: an open-source phosphorylation site assignment tool for MSn data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Using BiblioSpec for creating and searching tandem MS peptide libraries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

OpenMS - an open-source software framework for mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Analysis and validation of proteomic data generated by tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

YPED: a web-accessible database system for protein expression analysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

The minimum information about a proteomics experiment (MIAPE)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Quantitative mass spectrometry in proteomics: a critical review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A high-quality catalog of the Drosophila melanogaster proteome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A curated compendium of phosphorylation motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Automatic validation of phosphopeptide identifications from tandem mass spectra

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Detecting differential and correlated protein expression in label-free shotgun proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

PEPPeR, a platform for experimental proteomic pattern recognition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Probabilistic enrichment of phosphopeptides by their mass defect

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Software for computational peptide identification from MS-MS data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Using the global proteome machine for protein identification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

MapQuant: open-source software for large-scale protein quantification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Proteomics-grade de novo sequencing approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

MSight: an image analysis software for liquid chromatography-mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A common open representation of mass spectrometry data and its application to proteomics research

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Open mass spectrometry search algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Rapid identification of proteins by peptide-mass fingerprinting

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

TANDEM: matching proteins with tandem mass spectra

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

A statistical model for identifying proteins by tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Identifying biological themes within lists of genes with EASE

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Probability-based protein identification by searching sequence databases using mass spectrometry data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

De novo peptide sequencing via tandem mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Direct analysis of protein complexes using mass spectrometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

Error-tolerant identification of peptides in sequence databases by peptide sequence tags

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

De novo analysis of peptide tandem mass spectra by spectral graph partitioning.

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Quantitative mass spectrometry identifies insulin signaling targets in C. elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Prediction of phosphorylation sites using SVMs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Computational prediction of proteotypic peptides for quantitative proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Qscore: an algorithm for evaluating SEQUEST database search results

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Chromatographic retention time prediction for posttranslationally modified peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

EBP, a program for protein identification using multiple tandem mass spectrometry datasets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Code developments to improve the efficiency of automated MS/MS spectra interpretation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Universal and confident phosphorylation site localization using phosphoRS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

GPS: a novel group-based phosphorylation predicting and scoring method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Statistical Analysis of Membrane Proteome Expression Changes inSaccharomycescerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1321S41

Protein identification using a quadrupole ion trap mass spectrometer and SEQUEST database matching

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

ScanProsite: a reference implementation of a PROSITE scanning tool

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688054

MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23504934

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23504934

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/0471250953.BI1321S41

1 reference

14 November 2017

1 reference

14 November 2017

1 reference

PMCID

3688054