Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 170

The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

Arike, L., Valgepea, K., Peil, L., Nahku, R., Adamberg, K., Vilu, R.·2012·Journal of Proteomics
DOI 10.1016/j.jprot.2012.06.020
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.jprot.2012.06.020

Cites

15 of 15 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 15 references

Research works printed but not linked: 38

  1. Chelius, 2002, Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry, J Proteome Res, 317, 10.1021/pr025517j · DOI · Paper page
  2. Wang, 2003, Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards, Anal Chem, 75, 4818, 10.1021/ac026468x · DOI · Paper page
  3. Picotti, 2010, High-throughput generation of selected reaction-monitoring assays for proteins and proteomes, Nat Methods, 7, 43, 10.1038/nmeth.1408 · DOI · Paper page
  4. Hanke, 2008, Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level, J Proteome, 7, 1118, 10.1021/pr7007175 · DOI · Paper page
  5. Canas, 2007, Trends in sample preparation for classical and second generation proteomics, J Chromatogr A, 1153, 235, 10.1016/j.chroma.2007.01.045 · DOI
  6. Hirabayashi, 2007, Detection of potential ion suppression for peptide analysis in nanoflow liquid chromatography/mass spectrometry, Rapid Commun Mass Spectrom, 21, 2860, 10.1002/rcm.3157 · DOI
  7. King, 2000, Mechanistic investigation of ionization suppression in electrospray ionization, J Am Soc Mass Spectrom, 11, 942, 10.1016/S1044-0305(00)00163-X · DOI · Paper page
  8. Silva, 2005, Quantitative proteomic analysis by accurate mass retention time pairs, Anal Chem, 77, 2187, 10.1021/ac048455k · DOI · Paper page
  9. Neilson, 2011, Less label, more free: approaches in label-free quantitative mass spectrometry, Proteomics, 11, 535, 10.1002/pmic.201000553 · DOI · Paper page
  10. Elliott, 2009, Current trends in quantitative proteomics, J Mass Spectrom, 44, 1637, 10.1002/jms.1692 · DOI · Paper page
  11. Zhu, 2010, Mass spectrometry-based label-free quantitative proteomics, J Biomed Biotechnol, 2010, 840518, 10.1155/2010/840518 · DOI · Paper page
  12. Grossmann, 2010, Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods, J Proteomics, 73, 1740, 10.1016/j.jprot.2010.05.011 · DOI
  13. Ishihama, 2005, Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein, Mol Cell Proteomics, 4, 1265, 10.1074/mcp.M500061-MCP200 · DOI · Paper page
  14. Ishihama, 2008, Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, 9, 102, 10.1186/1471-2164-9-102 · DOI · Paper page
  15. Kuntumalla, 2009, Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome, Proteome Sci, 7, 22, 10.1186/1477-5956-7-22 · DOI · Paper page
  16. Schmidt, 2011, Absolute quantification of microbial proteomes at different states by directed mass spectrometry, Mol Syst Biol, 7, 1, 10.1038/msb.2011.37 · DOI
  17. Braisted, 2008, The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results, BMC Bioinformatics, 9, 529, 10.1186/1471-2105-9-529 · DOI
  18. Valgepea, 2010, Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase, BMC Syst Biol, 4, 166, 10.1186/1752-0509-4-166 · DOI
  19. Rappsilber, 2007, Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips, Nat Protoc, 2, 1896, 10.1038/nprot.2007.261 · DOI · Paper page
  20. Olsen, 2005, Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap, Mol Cell Proteomics, 4, 2010, 10.1074/mcp.T500030-MCP200 · DOI · Paper page
  21. Nesvizhskii, 2003, A statistical model for identifying proteins by tandem mass spectrometry, Anal Chem, 75, 4646, 10.1021/ac0341261 · DOI · Paper page
  22. Nahku, 2010, Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures, J Biotechnol, 145, 60, 10.1016/j.jbiotec.2009.10.007 · DOI
  23. Tatusov, 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41, 10.1186/1471-2105-4-41 · DOI · Paper page
  24. Keseler, 2011, EcoCyc: a comprehensive database of Escherichia coli biology, Nucleic Acids Res, 39, D583, 10.1093/nar/gkq1143 · DOI · Paper page
  25. Rice, 2000, EMBOSS: the European Molecular Biology Open Software Suite, Trends Genet, 16, 276, 10.1016/S0168-9525(00)02024-2 · DOI · Paper page
  26. Charif, 2005, Online synonymous codon usage analyses with the ade4 and seqinR packages, Bioinformatics (Oxford, England), 21, 545
  27. Stouthamer, 1973, A theoretical study on the amount of ATP required for synthesis of microbial cell material, Antonie Van Leeuwenhoek, 39, 545, 10.1007/BF02578899 · DOI · Paper page
  28. Hoehenwarter, 2010, Spectral counting robust on high mass accuracy mass spectrometers, Rapid Commun Mass Spectrom, 24, 3609, 10.1002/rcm.4818 · DOI
  29. Zhang, 2009, Effect of dynamic exclusion duration on spectral count based quantitative proteomics, Anal Chem, 81, 6317, 10.1021/ac9004887 · DOI · Paper page
  30. Adamberg, 2009, Quasi steady state growth of Lactococcus lactis in glucose-limited acceleration stat (A-stat) cultures, Antonie Van Leeuwenhoek, 95, 219, 10.1007/s10482-009-9305-z · DOI
  31. Lahtvee, 2011, Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates, Microb Cell Fact, 10, 12, 10.1186/1475-2859-10-12 · DOI
  32. Ishii, 2007, Multiple high-throughput analyses monitor the response of E. coli to perturbations, Science, 316, 593, 10.1126/science.1132067 · DOI · Paper page
  33. Masuda, 2009, Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants, Mol Cell Proteomics, 8, 2770, 10.1074/mcp.M900240-MCP200 · DOI
  34. Maier, 2011, Quantification of mRNA and protein and integration with protein turnover in a bacterium, Mol Syst Biol, 7, 1, 10.1038/msb.2011.38 · DOI · Paper page
  35. Coghlan, 2000, Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae, Yeast (Chichester, England), 16, 1131, 10.1002/1097-0061(20000915)16:12<1131::AID-YEA609>3.0.CO;2-F · DOI · Paper page
  36. Riley, 2006, Escherichia coli K-12: a cooperatively developed annotation snapshot—2005, Nucleic Acids Res, 34, 1, 10.1093/nar/gkj405 · DOI · Paper page
  37. Kozak, 1983, Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles, Microbiol Rev, 47, 1, 10.1128/mr.47.1.1-45.1983 · doi:10.1128/mr.47.1.1-45.1983 · Paper page
  38. Cho, 2009, The transcription unit architecture of the Escherichia coli genome, Nat Biotechnol, 27, 1043, 10.1038/nbt.1582 · DOI · Paper page

Cited by

See all 170

Metadata

Authors
Arike, L., Valgepea, K., Peil, L., Nahku, R., Adamberg, K., & Vilu, R.
Venue
Journal of Proteomics
Publisher
Elsevier BV
Published
2012-09
Volume
75
Issue
17
Pages
5437-5448
ISSN
1874-3919 (ISSN-L)
DOI
10.1016/j.jprot.2012.06.020
OpenAlex
W2094125753
Cited by
170
References
15
FWCI
7.32
Type
journal article
Language
en
Update notices
erratum (2013-10-08)
Open access
closed
Licence
  • www.elsevier.com/tdm/userlicense/1.0/ (tdm)
  • www.elsevier.com/legal/tdmrep-license (tdm)
Funders
Haridus- ja Teadusministeerium (SF0140090s08)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. https://app.cochat.ai/papers/10.1016/j.jprot.2012.06.020
The paper
Arike, L., Valgepea, K., Peil, L., Nahku, R., Adamberg, K., & Vilu, R. (2012). Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. Journal of Proteomics. https://doi.org/10.1016/j.jprot.2012.06.020

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.