(Q33229418)

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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

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scholarly article

1 reference

Europe PubMed Central

24 July 2017

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 (English)

1 reference

Europe PubMed Central

24 July 2017

Alexey I. Nesvizhskii

object named as

Alexey I Nesvizhskii

1

0 references

Wilhelm Gruissem

object named as

Wilhelm Gruissem

6

0 references

Ruedi Aebersold

8

object named as

Ruedi Aebersold

1 reference

Europe PubMed Central

24 July 2017

author name string

Franz F Roos

2

1 reference

Europe PubMed Central

24 July 2017

Jonas Grossmann

3

1 reference

Europe PubMed Central

24 July 2017

Mathijs Vogelzang

4

1 reference

Europe PubMed Central

24 July 2017

James S Eddes

5

1 reference

Europe PubMed Central

24 July 2017

Sacha Baginsky

7

1 reference

Europe PubMed Central

24 July 2017

publication date

12 December 2005

1 reference

Europe PubMed Central

24 July 2017

Molecular & Cellular Proteomics

1 reference

Europe PubMed Central

24 July 2017

5

1 reference

Europe PubMed Central

24 July 2017

652-670

1 reference

Europe PubMed Central

24 July 2017

4

1 reference

Europe PubMed Central

24 July 2017

Mass spectrometry-based proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Protein sequence databases

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Mass spectral analysis in proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Proteome analysis by mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Data analysis--the Achilles heel of proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Informatics for protein identification by mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

TANDEM: matching proteins with tandem mass spectra

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Open mass spectrometry search algorithm

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

OLAV: towards high-throughput tandem mass spectrometry data identification

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

A statistical model for identifying proteins by tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Protein identification by mass spectrometry: issues to be considered

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Sequence tag scanning: a new explorative strategy for recognition of unexpected protein alterations by nanoelectrospray ionization-tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Automatic quality assessment of peptide tandem mass spectra.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Spectral quality assessment for high-throughput tandem mass spectrometry proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the applicatio

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

The International Protein Index: an integrated database for proteomics experiments

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Preprocessing of tandem mass spectrometric data to support automatic protein identification

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Increased identification of peptides by enhanced data processing of high-resolution MALDI TOF/TOF mass spectra prior to database searching

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Interpretation of shotgun proteomic data: the protein inference problem

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

LIME: a new membrane Raft-associated adaptor protein involved in CD4 and CD8 coreceptor signaling

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

LIME, a novel transmembrane adaptor protein, associates with p56lck and mediates T cell activation

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Factors that affect ion trap data-dependent MS/MS in proteomics

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Detection of local polarity of alpha-lactalbumin by N-terminal specific labeling with a new tailor-made fluorescent probe

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

De novo peptide sequencing via tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

NovoHMM: a hidden Markov model for de novo peptide sequencing

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Peptide and protein de novo sequencing by mass spectrometry

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M500319-MCP200

21 January 2018

Identifiers

10.1074/MCP.M500319-MCP200

1 reference

Europe PubMed Central

24 July 2017

1 reference

Europe PubMed Central

24 July 2017

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