(Q47680249)

4 February 2018

title

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. (English)

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4 February 2018

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Lennart Martens

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4 February 2018

Harald Barsnes

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object named as

Harald Barsnes

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4 February 2018

author name string

Kenneth Verheggen

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4 February 2018

Helge Raeder

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4 February 2018

Frode S Berven

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4 February 2018

Marc Vaudel

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4 February 2018

publication date

13 September 2017

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4 February 2018

Mass Spectrometry Reviews

published in

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4 February 2018

Mass spectrometry-based proteomics

cites work

1 reference

Western blots versus selected reaction monitoring assays: time to turn the tables?

21 January 2018

1 reference

Electrospray ionization for mass spectrometry of large biomolecules

21 January 2018

1 reference

Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules

21 January 2018

1 reference

Protein and polymer analyses up tom/z 100 000 by laser ionization time-of-flight mass spectrometry

21 January 2018

1 reference

Effect of gas pressure and gas type on the fragmentation of peptide and oligosaccharide ions generated in an elevated pressure UV/IR-MALDI ion source coupled to an orthogonal time-of-flight mass spectrometer

21 January 2018

1 reference

Analysis of proteins and proteomes by mass spectrometry

21 January 2018

1 reference

In-depth evaluation of software tools for data-independent acquisition based label-free quantification

21 January 2018

1 reference

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

Collision-induced dissociation (CID) of peptides and proteins

21 January 2018

1 reference

Higher-energy C-trap dissociation for peptide modification analysis.

21 January 2018

1 reference

Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry

21 January 2018

1 reference

Computational methods for protein identification from mass spectrometry data

21 January 2018

1 reference

The mzIdentML data standard for mass spectrometry-based proteomics results

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Open mass spectrometry search algorithm

21 January 2018

1 reference

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes

21 January 2018

1 reference

Andromeda: a peptide search engine integrated into the MaxQuant environment

21 January 2018

1 reference

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

21 January 2018

1 reference

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra

21 January 2018

1 reference

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

21 January 2018

1 reference

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

21 January 2018

1 reference

mzML--a community standard for mass spectrometry data

21 January 2018

1 reference

File formats commonly used in mass spectrometry proteomics

21 January 2018

1 reference

A cross-platform toolkit for mass spectrometry and proteomics

21 January 2018

1 reference

A noise model for mass spectrometry based proteomics.

21 January 2018

1 reference

Accurate peak list extraction from proteomic mass spectra for identification and profiling studies.

21 January 2018

1 reference

Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data

21 January 2018

1 reference

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification.

21 January 2018

1 reference

Comparison of database search strategies for high precursor mass accuracy MS/MS data

21 January 2018

1 reference

OpenMS - an open-source software framework for mass spectrometry

21 January 2018

1 reference

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert

21 January 2018

1 reference

Crowdsourcing in proteomics: public resources lead to better experiments

21 January 2018

1 reference

Exploring the potential of public proteomics data

21 January 2018

1 reference

Mass spectrometric protein identification using the global proteome machine.

21 January 2018

1 reference

Making proteomics data accessible and reusable: current state of proteomics databases and repositories

21 January 2018

1 reference

PRIDE: the proteomics identifications database

21 January 2018

1 reference

2016 update of the PRIDE database and its related tools

21 January 2018

1 reference

Open source system for analyzing, validating, and storing protein identification data

21 January 2018

1 reference

Analysis of high accuracy, quantitative proteomics data in the MaxQB database

21 January 2018

1 reference

21 January 2018

The PeptideAtlas project

1 reference

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

21 January 2018

1 reference

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

21 January 2018

1 reference

UniProt: a hub for protein information

21 January 2018

1 reference

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

21 January 2018

1 reference

DNA data bank of Japan (DDBJ) progress report

21 January 2018

1 reference

Gene Ontology annotations at SGD: new data sources and annotation methods

21 January 2018

1 reference

TB database: an integrated platform for tuberculosis research

21 January 2018

1 reference

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

21 January 2018

1 reference

FlyBase 101--the basics of navigating FlyBase

21 January 2018

1 reference

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

21 January 2018

1 reference

WormBase 2014: new views of curated biology

21 January 2018

1 reference

The neXtProt knowledgebase on human proteins: current status

21 January 2018

1 reference

The Pathogen-Host Interactions database (PHI-base): additions and future developments

21 January 2018

1 reference

Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus

21 January 2018

1 reference

The effect of using an inappropriate protein database for proteomic data analysis

21 January 2018

1 reference

Reanalysis of Tyrannosaurus rex Mass Spectra

21 January 2018

1 reference

A stringent approach to improve the quality of nitrotyrosine peptide identifications.

21 January 2018

1 reference

Proteogenomics: concepts, applications and computational strategies

21 January 2018

1 reference

Databases of homologous gene families for comparative genomics

21 January 2018

1 reference

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

21 January 2018

1 reference

Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

21 January 2018

1 reference

Shedding light on black boxes in protein identification

21 January 2018

1 reference

Analysis of the resolution limitations of peptide identification algorithms.

21 January 2018

1 reference

Navigating through metaproteomics data: a logbook of database searching

21 January 2018

1 reference

Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra

21 January 2018

1 reference

Effectively addressing complex proteomic search spaces with peptide spectrum matching.

21 January 2018

1 reference

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

21 January 2018

1 reference

High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity.

21 January 2018

1 reference

Phosphoproteomics--more than meets the eye.

21 January 2018

1 reference

Proposal for a common nomenclature for sequence ions in mass spectra of peptides

21 January 2018

1 reference

ProbSeq--a fragmentation model for interpretation of electrospray tandem mass spectrometry data

21 January 2018

1 reference

Fragmentation pathways of protonated peptides

21 January 2018

1 reference

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

21 January 2018

1 reference

Expert system for computer-assisted annotation of MS/MS spectra

21 January 2018

1 reference

Machine learning methods for predictive proteomics

21 January 2018

1 reference

Re-fraction: a machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics

21 January 2018

1 reference

Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines.

21 January 2018

1 reference

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book

21 January 2018

1 reference

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

21 January 2018

1 reference

Fast multi-blind modification search through tandem mass spectrometry

21 January 2018

1 reference

TagRecon: high-throughput mutation identification through sequence tagging

21 January 2018

1 reference

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.

21 January 2018

1 reference

Machine learning applications in proteomics research: how the past can boost the future

21 January 2018

1 reference

A fast SEQUEST cross correlation algorithm

21 January 2018

1 reference

Error tolerant searching of uninterpreted tandem mass spectrometry data

21 January 2018

1 reference

Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies".

21 January 2018

1 reference

False discovery rates in spectral identification

21 January 2018

1 reference

Mass spectrometrists should search only for peptides they care about

21 January 2018

1 reference

Tandem Mass Spectrum Identification via Cascaded Search

21 January 2018

1 reference

More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

21 January 2018

1 reference

Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies.

21 January 2018

1 reference

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

21 January 2018

1 reference

A guided tour of the Trans-Proteomic Pipeline

21 January 2018

1 reference

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

21 January 2018

1 reference

Current methods for global proteome identification

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

A decoy-free approach to the identification of peptides

21 January 2018

1 reference

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

21 January 2018

1 reference

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

21 January 2018

1 reference

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines

21 January 2018

1 reference

Combining results of multiple search engines in proteomics

21 January 2018

1 reference

Using annotated peptide mass spectrum libraries for protein identification

21 January 2018

1 reference

Protein identification by spectral networks analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

21 January 2018

1 reference

De novo sequencing of peptides by MS/MS.

21 January 2018

1 reference

Algorithms for the de novo sequencing of peptides from tandem mass spectra

21 January 2018

1 reference

Lessons in de novo peptide sequencing by tandem mass spectrometry

21 January 2018

1 reference

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

21 January 2018

1 reference

Interpretation of shotgun proteomic data: the protein inference problem

21 January 2018

1 reference

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

21 January 2018

1 reference

ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

21 January 2018

1 reference

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory

21 January 2018

1 reference

Galaxy: a platform for interactive large-scale genome analysis

21 January 2018

1 reference

Multi-omic data analysis using Galaxy.

21 January 2018

1 reference

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

21 January 2018

1 reference

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline

21 January 2018

1 reference

A draft map of the human proteome

21 January 2018

1 reference

Mass-spectrometry-based draft of the human proteome

21 January 2018

1 reference

Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis.

21 January 2018

1 reference

In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism.

21 January 2018

1 reference

A human interactome in three quantitative dimensions organized by stoichiometries and abundances

21 January 2018

1 reference

Proteogenomic mapping as a complementary method to perform genome annotation

21 January 2018

1 reference

sORFs.org: a repository of small ORFs identified by ribosome profiling.

21 January 2018

1 reference

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

21 January 2018

1 reference

A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases

21 January 2018

1 reference

OLAV: towards high-throughput tandem mass spectrometry data identification

21 January 2018

1 reference

Interpreting peptide mass spectra by VEMS.

21 January 2018

1 reference

TANDEM: matching proteins with tandem mass spectra

21 January 2018

1 reference

ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer

21 January 2018

1 reference

DBDigger: reorganized proteomic database identification that improves flexibility and speed

21 January 2018

1 reference

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry

21 January 2018

1 reference

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

21 January 2018

1 reference

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

21 January 2018

1 reference

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

21 January 2018

1 reference

Rapid and accurate peptide identification from tandem mass spectra

21 January 2018

1 reference

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

21 January 2018

1 reference

A new probabilistic database search algorithm for ETD spectra

21 January 2018

1 reference

MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data

21 January 2018

1 reference

MacroSEQUEST: efficient candidate-centric searching and high-resolution correlation analysis for large-scale proteomics data sets

21 January 2018

1 reference

Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides

21 January 2018

1 reference

Faster SEQUEST searching for peptide identification from tandem mass spectra

21 January 2018

1 reference

MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry

21 January 2018

1 reference

SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry

21 January 2018

1 reference

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

21 January 2018

1 reference

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification

21 January 2018

1 reference

Tempest: GPU-CPU computing for high-throughput database spectral matching

21 January 2018

1 reference

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra

21 January 2018

1 reference

Comet: an open-source MS/MS sequence database search tool

21 January 2018

1 reference

Why phosphoproteomics is still a challenge

21 January 2018

1 reference

Peptide identification quality control

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/MAS.21543

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4 February 2018

PubMed ID

28902424

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4 February 2018