Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation (Q24676843)

8

0 references

Nitin Gupta

Nitin Gupta

1

0 references

Margaret F Romine

Margaret Romine

7

0 references

Vineet Bafna

Vineet Bafna

9

0 references

Richard D. Smith

Richard D Smith

10

0 references

Pavel A. Pevzner

11

Pavel A Pevzner

0 references

Mary S Lipton

5

Mary Lipton

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author name string

Stephen Tanner

2

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Navdeep Jaitly

3

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Joshua N Adkins

4

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Robert Edwards

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

6

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language of work or name

English

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publication date

September 2007

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published in

Genome Research

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volume

17

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issue

9

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page(s)

1362-77

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cites work

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7 April 2017

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Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

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A new UAG-encoded residue in the structure of a methanogen methyltransferase

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Environmental genome shotgun sequencing of the Sargasso Sea

7 April 2017

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Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

7 April 2017

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Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

7 April 2017

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Mass spectrometry allows direct identification of proteins in large genomes

7 April 2017

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Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry

7 April 2017

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Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon

7 April 2017

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Isolation of glutamic acid methyl ester from an Escherichia coli membrane protein involved in chemotaxis

7 April 2017

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7 April 2017

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The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

7 April 2017

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

7 April 2017

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Interpreting the protein language using proteomics.

28 September 2017

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

28 September 2017

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Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias.

28 September 2017

1 reference

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Identification of degradation products formed during performic oxidation of peptides and proteins by high-performance liquid chromatography with matrix-assisted laser desorption/ionization and tandem mass spectrometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

28 September 2017

1 reference

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PrediSi: prediction of signal peptides and their cleavage positions

28 September 2017

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The RESID Database of Protein Modifications as a resource and annotation tool

28 September 2017

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Comparative genomics, minimal gene-sets and the last universal common ancestor

28 September 2017

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Reannotation of Shewanella oneidensis Genome

28 September 2017

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28 September 2017

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Breathing metals as a way of life: geobiology in action

28 September 2017

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The relative rates of glutamine and asparagine deamidation in glucagon fragment 22-29 under acidic conditions

28 September 2017

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Parallel identification of new genes in Saccharomyces cerevisiae

28 September 2017

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Recoding: translational bifurcations in gene expression.

28 September 2017

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The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors

28 September 2017

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Characterization of intact microorganisms by MALDI mass spectrometry

28 September 2017

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A proteomic view on genome-based signal peptide predictions

28 September 2017

1 reference

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

28 September 2017

1 reference

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High-throughput mass spectrometric discovery of protein post-translational modifications.

28 September 2017

1 reference

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Translation of the flagellar gene fliO of Salmonella typhimurium from putative tandem starts.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

Molecular cloning and sequencing of infC, the gene encoding translation initiation factor IF3, from four enterobacterial species

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

Methylation of the Flagellin of Salmonella typhimurium

28 September 2017

1 reference

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Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure

28 September 2017

1 reference

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The N-end rule in bacteria.

28 September 2017

1 reference

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Location of the site of methylation in elongation factor Tu

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

50 Dipeptidyl carboxypeptidase from Escherichia coli

28 September 2017

1 reference

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Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1950905

Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis

30 May 2018

1 reference

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Proteogenomic mapping as a complementary method to perform genome annotation

30 May 2018

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Small genes/gene-products in Escherichia coli K-12.

30 May 2018

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Degradative covalent reactions important to protein stability

30 May 2018

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Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

30 May 2018

1 reference

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Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo

30 May 2018

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The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli.

30 May 2018

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Beta-methylthio-aspartic acid: identification of a novel posttranslational modification in ribosomal protein S12 from Escherichia coli

30 May 2018

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Identification of a putative infC-rpmI-rplT operon flanked by long inverted repeats in Mycoplasma fermentans (incognitus strain).

30 May 2018

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Cloning and characterization of a gene cluster from Bacillus stearothermophilus comprising infC, rpmI and rplT.

30 May 2018

1 reference

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Amino acids responsible for flagellar shape are distributed in terminal regions of flagellin.

30 May 2018

1 reference

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Unrestrictive identification of post-translational modifications through peptide mass spectrometry

30 May 2018

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The proteomics of N-terminal methionine cleavage.

28 November 2018

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A computational approach toward label-free protein quantification using predicted peptide detectability.

28 November 2018

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Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis

28 November 2018

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Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1.

28 November 2018

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Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics.

28 November 2018

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InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

28 November 2018

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28 November 2018

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Trypsin cleaves exclusively C-terminal to arginine and lysine residues

28 November 2018

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Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps

28 November 2018

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Overalkylation of a protein digest with iodoacetamide.

28 November 2018

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The Comprehensive Microbial Resource.

28 November 2018

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The identification of peptide modifications derived from gel-separated proteins using electrospray triple quadrupole and ion trap analyses

28 November 2018

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Methylation of ribosomal proteins during ribosome assembly in Escherichia coli

28 November 2018

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12 December 2020

Multiple covalent modifications of Trg, a sensory transducer of Escherichia coli

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Influence of ions on cyclization of the amino terminal glutamine residues of tryptic peptides of streptococcal PepM49 protein. Resolution of cyclized peptides by HPLC and characterization by mass spectrometry

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Strategies for determination of disulphide bridges in proteins using plasma desorption mass spectrometry

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Identification of an artifact in the mass spectrometry of proteins derivatized with iodoacetamide

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Deamidation as a widespread phenomenon in two-dimensional polyacrylamide gel electrophoresis of human blood plasma proteins

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Purified human growth hormone from E. coli is biologically active

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Carbamylation of cysteine: a potential artifact in peptide mapping of hemoglobins in the presence of urea

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Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases

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Identification of oxidized methionine in peptides

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

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Identifiers

DOI

10.1101/GR.6427907

1 reference

2661302

2661302

1 reference

1 reference

1 reference