(Q34207316)

31 July 2017

title

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

1 reference

31 July 2017

main subject

computational biology

1 reference

1 reference

Alexey I. Nesvizhskii

object named as

Alexey I Nesvizhskii

series ordinal

1

0 references

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=20816881

6 July 2024

publication date

8 September 2010

1 reference

full work available at URL

31 July 2017

https://europepmc.org/articles/pmc2956504?pdf=render

file format

Portable Document Format

online access status

open access

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https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20816881/pdf/?tool=EBI

6 July 2024

file format

Portable Document Format

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20816881

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20816881/?tool=EBI

6 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20816881

https://europepmc.org/articles/PMC2956504

6 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20816881

https://europepmc.org/articles/PMC2956504?pdf=render

6 July 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20816881

https://doi.org/10.1016/j.jprot.2010.08.009

6 July 2024

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20816881

https://api.elsevier.com/content/article/PII:S1874391910002496?httpAccept=text/xml

6 July 2024

1 reference

Crossref

https://api.crossref.org/works/10.1016/J.JPROT.2010.08.009

https://api.elsevier.com/content/article/PII:S1874391910002496?httpAccept=text/plain

6 July 2024

1 reference

Crossref

https://api.crossref.org/works/10.1016/J.JPROT.2010.08.009

6 July 2024

published in

Journal of Proteomics

1 reference

31 July 2017

volume

73

1 reference

31 July 2017

issue

11

1 reference

31 July 2017

page(s)

2092-2123

1 reference

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

31 July 2017

cites work

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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TagRecon: high-throughput mutation identification through sequence tagging

28 July 2018

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28 July 2018

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A guided tour of the Trans-Proteomic Pipeline

28 July 2018

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Data maximization by multipass analysis of protein mass spectra

28 July 2018

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Phosphoproteomics for the masses

28 July 2018

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Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry

28 July 2018

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Unrestricted identification of modified proteins using MS/MS.

28 July 2018

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What does the future hold for Top Down mass spectrometry?

28 July 2018

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Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations

28 July 2018

1 reference

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Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics

28 July 2018

1 reference

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A ubiquitin and ubiquitin-like protein spectral library

28 July 2018

1 reference

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Proteomics data repositories

28 July 2018

1 reference

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Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets

28 July 2018

1 reference

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Network-assisted protein identification and data interpretation in shotgun proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A bayesian approach to protein inference problem in shotgun proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Mining gene functional networks to improve mass-spectrometry-based protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

NCBI Peptidome: a new public repository for mass spectrometry peptide identifications

28 July 2018

1 reference

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Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function.

28 July 2018

1 reference

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

28 July 2018

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

28 July 2018

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

28 July 2018

1 reference

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A new probabilistic database search algorithm for ETD spectra

28 July 2018

1 reference

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Accurate and sensitive peptide identification with Mascot Percolator

28 July 2018

1 reference

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Integrating shotgun proteomics and mRNA expression data to improve protein identification

28 July 2018

1 reference

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Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

28 July 2018

1 reference

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Statistical calibration of the SEQUEST XCorr function

28 July 2018

1 reference

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Phosphoproteomics: miles to go before it's routine

28 July 2018

1 reference

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Predicting intensity ranks of peptide fragment ions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

28 July 2018

1 reference

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A simple workflow to increase MS2 identification rate by subsequent spectral library search

28 July 2018

1 reference

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A ranking-based scoring function for peptide-spectrum matches

28 July 2018

1 reference

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The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

28 July 2018

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Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

28 July 2018

1 reference

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Predictions of peptides' retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomics

28 July 2018

1 reference

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PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites.

28 July 2018

1 reference

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A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins

28 July 2018

1 reference

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Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification

28 July 2018

1 reference

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Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

28 July 2018

1 reference

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

28 July 2018

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Proteomics studies confirm the presence of alternative protein isoforms on a large scale

28 July 2018

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Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics

28 July 2018

1 reference

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Selected reaction monitoring for quantitative proteomics: a tutorial

28 July 2018

1 reference

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

28 July 2018

1 reference

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Simplified validation of borderline hits of database searches

28 July 2018

1 reference

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Building consensus spectral libraries for peptide identification in proteomics

28 July 2018

1 reference

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Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics

28 July 2018

1 reference

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Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications

28 July 2018

1 reference

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Improved sequence tag generation method for peptide identification in tandem mass spectrometry

28 July 2018

1 reference

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De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins

28 July 2018

1 reference

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Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics

28 July 2018

1 reference

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Precursor-ion mass re-estimation improves peptide identification on hybrid instruments

28 July 2018

1 reference

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Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra

28 July 2018

1 reference

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Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

SeMoP: a new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data

28 July 2018

1 reference

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A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data

28 July 2018

1 reference

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Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

28 July 2018

1 reference

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In-depth analysis of tandem mass spectrometry data from disparate instrument types

28 July 2018

1 reference

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Improved ranking functions for protein and modification-site identifications

28 July 2018

1 reference

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Significance analysis of spectral count data in label-free shotgun proteomics

28 July 2018

1 reference

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Protein identification pipeline for the homology-driven proteomics.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Quantitative phosphoproteomic analysis of signaling network dynamics.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Detection of co-eluted peptides using database search methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Enhancing peptide identification confidence by combining search methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Monte carlo simulation-based algorithms for analysis of shotgun proteomic data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Modes of inference for evaluating the confidence of peptide identifications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Posterior error probabilities and false discovery rates: two sides of the same coin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Calibrating E-values for MS2 database search methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

RAId_DbS: peptide identification using database searches with realistic statistics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Mapping protein post-translational modifications with mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

How do shotgun proteomics algorithms identify proteins?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A platform for accurate mass and time analyses of mass spectrometry data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A high-quality catalog of the Drosophila melanogaster proteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Protein identification by spectral networks analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

De novo peptide sequencing and identification with precision mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improving gene annotation using peptide mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Protein identification by tandem mass spectrometry and sequence database searching

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Using annotated peptide mass spectrum libraries for protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A fast coarse filtering method for peptide identification by mass spectrometry.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Identification of post-translational modifications by blind search of mass spectra.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

PRIDE: the proteomics identifications database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Interpretation of shotgun proteomic data: the protein inference problem

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

The use of proteotypic peptide libraries for protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliab

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by s

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

DBParser: web-based software for shotgun proteomic data analyses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Open mass spectrometry search algorithm

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

The ABC's (and XYZ's) of peptide sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

TANDEM: matching proteins with tandem mass spectra

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A statistical model for identifying proteins by tandem mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Protein identification by mass spectrometry: issues to be considered

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Preprocessing of tandem mass spectrometric data to support automatic protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

OLAV: towards high-throughput tandem mass spectrometry data identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Statistical significance for genomewide studies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

PRISM, a generic large scale proteomic investigation strategy for mammals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Mass spectrometry-based proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Data analysis--the Achilles heel of proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

What does it mean to identify a protein in proteomics?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Peptide sequence motif analysis of tandem MS data with the SALSA algorithm

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Interrogating the human genome using uninterpreted mass spectrometry data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Significance analysis of microarrays applied to the ionizing radiation response

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

pNovo: de novo peptide sequencing and identification using HCD spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

OVNIp: an open source application facilitating the interpretation, the validation and the edition of proteomics data generated by MS analyses and de novo sequencing

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Prediction of electron-transfer/capture dissociation spectra of peptides.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Detection of alternative splice variants at the proteome level in Aspergillus flavus

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

De novo sequencing of peptides by MS/MS.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A software program for more reliable precursor ion assignation from LC-MS analysis using LTQ ultra zoom scan

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A refined method to calculate false discovery rates for peptide identification using decoy databases.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Spectrum fusion: using multiple mass spectra for de novo Peptide sequencing

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Increased confidence in large-scale phosphoproteomics data by complementary mass spectrometric techniques and matching of phosphopeptide data sets

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Proteomics by mass spectrometry: approaches, advances, and applications

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Post-acquisition ETD spectral processing for increased peptide identifications

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

SLoMo: automated site localization of modifications from ETD/ECD mass spectra.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A spectral clustering approach to MS/MS identification of post-translational modifications

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Nonlinear fitting method for determining local false discovery rates from decoy database searches.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Rapid and accurate peptide identification from tandem mass spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Properties of average score distributions of SEQUEST: the probability ratio method.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

CIFTER: automated charge-state determination for peptide tandem mass spectra.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A nonparametric model for quality control of database search results in shotgun proteomics

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Charger: combination of signal processing and statistical learning algorithms for precursor charge-state determination from electron-transfer dissociation spectra.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Accurate annotation of peptide modifications through unrestrictive database search

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Quantitative mass spectrometry in proteomics: a critical review

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Large-scale unrestricted identification of post-translation modifications using tandem mass spectrometry.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Computational prediction of proteotypic peptides for quantitative proteomics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improved validation of peptide MS/MS assignments using spectral intensity prediction.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Reporting protein identification data: the next generation of guidelines.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Peptide sequence tags for fast database search in mass-spectrometry.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

PepNovo: de novo peptide sequencing via probabilistic network modeling

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

28 October 2018

Proteomic informatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Trypsin cleaves exclusively C-terminal to arginine and lysine residues

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Intensity-based protein identification by machine learning from a library of tandem mass spectra.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Improved peptide charge state assignment.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Biomedical informatics for proteomics

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Intensity-based statistical scorer for tandem mass spectrometry.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

Reproducible isolation of distinct, overlapping segments of the phosphoproteome

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956504

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

28 October 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm

1 reference

12 December 2020

PeptideClassifier for protein inference and targeted quantitative proteomics

1 reference

12 December 2020

Experiments in searching small proteins in unannotated large eukaryotic genomes

1 reference

12 December 2020

The implications of proteolytic background for shotgun proteomics

1 reference

12 December 2020

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

1 reference

12 December 2020

Extent of Modifications in Human Proteome Samples and Their Effect on Dynamic Range of Analysis in Shotgun Proteomics

1 reference

12 December 2020

Target-Decoy with Mass Binning: a simple and effective validation method for shotgun proteomics using high resolution mass spectrometry

1 reference

12 December 2020

Estimating the confidence of peptide identifications without decoy databases

1 reference

12 December 2020

Unbiased statistical analysis for multi-stage proteomic search strategies

1 reference

12 December 2020

A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments

1 reference

12 December 2020

Empirical Bayes Analysis of a Microarray Experiment

series ordinal

173

1 reference

Crossref

https://api.crossref.org/works/10.1016/J.JPROT.2010.08.009

6 July 2024

Identifiers

1 reference

31 July 2017

1 reference

31 July 2017

1 reference