(Q31131394)

29 June 2017

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title

Analysis and validation of proteomic data generated by tandem mass spectrometry (English)

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29 June 2017

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Alexey I. Nesvizhskii

object named as

Alexey I Nesvizhskii

series ordinal

1

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Ruedi Aebersold

series ordinal

3

object named as

Ruedi Aebersold

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29 June 2017

Olga Vitek

2

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29 June 2017

1 October 2007

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29 June 2017

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29 June 2017

4

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29 June 2017

787-797

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29 June 2017

10

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Mass spectrometry-based proteomics

29 June 2017

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7 January 2021

Mass spectrometry and protein analysis

1 reference

7 January 2021

The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.

1 reference

7 January 2021

Open mass spectrometry search algorithm

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

1 reference

7 January 2021

A high-quality catalog of the Drosophila melanogaster proteome

1 reference

7 January 2021

Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis

1 reference

7 January 2021

Using annotated peptide mass spectrum libraries for protein identification

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

Optimization and testing of mass spectral library search algorithms for compound identification

1 reference

7 January 2021

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

1 reference

7 January 2021

Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

Statistical significance for genomewide studies

1 reference

7 January 2021

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

1 reference

7 January 2021

Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations

1 reference

7 January 2021

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.

1 reference

7 January 2021

A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics: Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores

1 reference

7 January 2021

PRISM, a generic large scale proteomic investigation strategy for mammals

1 reference

7 January 2021

Improved classification of mass spectrometry database search results using newer machine learning approaches

1 reference

7 January 2021

Preprocessing of tandem mass spectrometric data to support automatic protein identification

1 reference

7 January 2021

Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise.

1 reference

7 January 2021

Improving large-scale proteomics by clustering of mass spectrometry data.

1 reference

7 January 2021

MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

1 reference

7 January 2021

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

1 reference

7 January 2021

Method for screening peptide fragment ion mass spectra prior to database searching

1 reference

7 January 2021

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics.

1 reference

7 January 2021

Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering

1 reference

7 January 2021

Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry

1 reference

7 January 2021

Improved peptide charge state assignment.

1 reference

7 January 2021

Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.

1 reference

7 January 2021

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

1 reference

7 January 2021

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

1 reference

7 January 2021

Estimating the statistical significance of peptide identifications from shotgun proteomics experiments.

1 reference

7 January 2021

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

1 reference

7 January 2021

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation

1 reference

7 January 2021

Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry

1 reference

7 January 2021

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome

1 reference

7 January 2021

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.

1 reference

7 January 2021

Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics

1 reference

7 January 2021

Gel based isoelectric focusing of peptides and the utility of isoelectric point in protein identification.

1 reference

7 January 2021

High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry

1 reference

7 January 2021

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

1 reference

7 January 2021

Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap

1 reference

7 January 2021

Large scale analysis of MASCOT results using a Mass Accuracy-based THreshold (MATH) effectively improves data interpretation

1 reference

7 January 2021

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.

1 reference

7 January 2021

Interpretation of shotgun proteomic data: the protein inference problem

1 reference

7 January 2021

A statistical model for identifying proteins by tandem mass spectrometry

1 reference

7 January 2021

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

1 reference

7 January 2021

What does it mean to identify a protein in proteomics?

1 reference

7 January 2021

DBParser: web-based software for shotgun proteomic data analyses

1 reference

7 January 2021

A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results

1 reference

7 January 2021

Protein identification by spectral networks analysis

1 reference

7 January 2021

Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study

1 reference

7 January 2021

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases

1 reference

7 January 2021

Computational prediction of proteotypic peptides for quantitative proteomics.

1 reference

7 January 2021

Stable isotope-coded proteomic mass spectrometry

1 reference

7 January 2021

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

1 reference

7 January 2021

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

1 reference

7 January 2021

Correlation of Relative Abundance Ratios Derived from Peptide Ion Chromatograms and Spectrum Counting for Quantitative Proteomic Analysis Using Stable Isotope Labeling

1 reference

7 January 2021

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

1 reference

7 January 2021

Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition

1 reference

7 January 2021

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

1 reference

7 January 2021

Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling

1 reference

7 January 2021

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

1 reference

7 January 2021

PEPPeR, a platform for experimental proteomic pattern recognition.

1 reference

7 January 2021

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry

1 reference

7 January 2021

Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry

1 reference

7 January 2021

Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications

1 reference

7 January 2021

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins

1 reference

7 January 2021

Bioconductor: open software development for computational biology and bioinformatics

1 reference

7 January 2021

Detection and localization of protein modifications by high resolution tandem mass spectrometry

1 reference

7 January 2021

Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons

1 reference

7 January 2021

Chemistry. Mass spectrometry: bottom-up or top-down?

1 reference

7 January 2021

Scoring proteomes with proteotypic peptide probes

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.

1 reference

7 January 2021

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

1 reference

7 January 2021

TANDEM: matching proteins with tandem mass spectra

1 reference

7 January 2021

OLAV: towards high-throughput tandem mass spectrometry data identification

1 reference

7 January 2021

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

1 reference

7 January 2021

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

1 reference

7 January 2021

The use of proteotypic peptide libraries for protein identification

1 reference

7 January 2021

Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry

1 reference

7 January 2021

PepNovo: de novo peptide sequencing via probabilistic network modeling

1 reference

7 January 2021

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

1 reference

7 January 2021

Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data

1 reference

7 January 2021

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

1 reference

7 January 2021

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

1 reference

7 January 2021

PRIDE: the proteomics identifications database

1 reference

7 January 2021

Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry

1 reference

7 January 2021

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data

1 reference

7 January 2021

Significance analysis of microarrays applied to the ionizing radiation response

1 reference

7 January 2021

Empirical Bayes Analysis of a Microarray Experiment

1 reference

7 January 2021

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

1 reference

7 January 2021

Improving gene annotation using peptide mass spectrometry

1 reference

7 January 2021

Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

1 reference

7 January 2021

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

1 reference

7 January 2021

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

1 reference

7 January 2021

Identifiers

DOI

10.1038/NMETH1088

1 reference

PubMed ID

17901868

Dimensions Publication ID

29 June 2017

0 references

1 reference

PubMed ID

17901868