Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 258

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

Ion Coalescence of Neutron Encoded TMT 10-Plex Reporter Ions

Werner, Thilo, Sweetman, Gavain, Savitski, Maria Fälth, Mathieson, Toby, Bantscheff, Marcus, Savitski, Mikhail M·2014·Analytical Chemistry
DOI 10.1021/ac500140s
Open this paper in CoChat — free account

Abstract

Isobaric mass tag-based quantitative proteomics strategies such as iTRAQ and TMT utilize reporter ions in the low mass range of tandem MS spectra for relative quantification. The recent extension of TMT multiplexing to 10 conditions has been enabled by utilizing neutron encoded tags with reporter ion m/z differences of 6 mDa. The baseline resolution of these closely spaced tags is possible due to the high resolving power of current day mass spectrometers. In this work we evaluated the performance of the TMT10 isobaric mass tags on the Q Exactive Orbitrap mass spectrometers for the first time and demonstrated comparable quantification accuracy and precision to what can be achieved on the Orbitrap Elite mass spectrometers. However, we discovered, upon analysis of complex proteomics samples on the Q Exactive Orbitrap mass spectrometers, that the proximate TMT10 reporter ion pairs become prone to coalescence. The fusion of the different reporter ion signals into a single measurable entity has a detrimental effect on peptide and protein quantification. We established that the main reason for coalescence is the commonly accepted maximum ion target for MS2 spectra of 1e6 on the Q Exactive instruments. The coalescence artifact was completely removed by lowering the maximum ion target for MS2 spectra from 1e6 to 2e5 without any losses in identification depth or quantification quality of proteins.

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 · 10.1021/ac500140s

Cites

8 of 8 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 8 references

Research works printed but not linked: 35

  1. Bantscheff M., 2007, Anal. Bioanal. Chem., 389, 1017, 10.1007/s00216-007-1486-6 · DOI · Paper page
  2. Pflieger D., 2008, Mol. Cell. Proteomics, 7, 326, 10.1074/mcp.M700282-MCP200 · DOI
  3. Przybylski C., 2010, J. Proteome Res., 9, 5118, 10.1021/pr1003888 · DOI
  4. Iwai L. K., 2010, J. Proteome Res., 9, 3135, 10.1021/pr100035b · DOI
  5. Olsen J. V., 2006, Cell, 127, 635, 10.1016/j.cell.2006.09.026 · DOI · Paper page
  6. Rubbi L., 2011, Sci. Signaling, 4, ra18, 10.1126/scisignal.2001314 · DOI
  7. Bantscheff M., 2007, Nat. Biotechnol., 25, 1035, 10.1038/nbt1328 · DOI · Paper page
  8. Bantscheff M., 2009, Drug Discov. Today, 14, 1021, 10.1016/j.drudis.2009.07.001 · DOI
  9. Patricelli M. P., 2011, Chem. Biol., 18, 699, 10.1016/j.chembiol.2011.04.011 · DOI · Paper page
  10. Remsing Rix L. L., 2009, Leukemia, 23, 477, 10.1038/leu.2008.334 · DOI · Paper page
  11. Afkarian M., 2010, Mol. Cell. Proteomics, 9, 2195, 10.1074/mcp.M110.000992 · DOI
  12. Chao T. C., 2010, J. Proteomics, 73, 1641, 10.1016/j.jprot.2010.04.004 · DOI
  13. Schiess R., 2009, Mol. Oncol., 3, 33, 10.1016/j.molonc.2008.12.001 · DOI · Paper page
  14. Turtoi A., 2011, J. Proteome Res., 10, 3160, 10.1021/pr200212r · doi:10.1021/pr200212r
  15. Ye H., 2010, Mol. Cell. Biochem., 343, 91, 10.1007/s11010-010-0502-x · doi:10.1007/s11010-010-0502-x
  16. Thompson A., 2003, Anal. Chem., 75, 1895, 10.1021/ac0262560 · DOI · Paper page
  17. Dayon L., 2008, Anal. Chem., 80, 2921, 10.1021/ac702422x · DOI · Paper page
  18. Werner T., 2012, Anal. Chem., 84, 7188, 10.1021/ac301553x · DOI
  19. Hebert A. S., 2013, Nat. Methods, 10, 332, 10.1038/nmeth.2378 · DOI
  20. Hebert A. S., 2013, Mol. Cell. Proteomics, 12, 3360, 10.1074/mcp.M113.032011 · DOI
  21. 10.1074/mcp.O1111.013698 · doi:10.1074/mcp.o1111.013698
  22. Boldin I. A., 2009, Rapid Commun. Mass Spectrom., 23, 3213, 10.1002/rcm.4231 · DOI
  23. Gorshkov M. V., 2012, Rapid Commun. Mass Spectrom., 26, 1711, 10.1002/rcm.6289 · DOI
  24. Scigelova M., 2011, Mol Cell Proteomics, 10, M111.009431, 10.1074/mcp.M111.009431 · DOI · Paper page
  25. Kruse U., 2011, Leukemia, 25, 89, 10.1038/leu.2010.233 · DOI
  26. Pachl F., 2012, Proteomics, 12, 1328, 10.1002/pmic.201100622 · DOI
  27. Savitski M. M., 2011, Anal. Chem., 83, 8959, 10.1021/ac201760x · DOI
  28. Savitski M. M., 2010, J. Am. Soc. Mass Spectrom., 21, 1668, 10.1016/j.jasms.2010.01.012 · DOI
  29. Savitski M. M., 2013, J. Proteome Res., 12, 3586, 10.1021/pr400098r · DOI · Paper page
  30. Becher I., 2013, ACS Chem. Biol., 8, 599, 10.1021/cb3005879 · DOI
  31. Kelstrup C. D., 2012, J. Proteome Res., 11, 3487, 10.1021/pr3000249 · DOI · Paper page
  32. Wiśniewski J. R., 2013, Proteomics: Clin. Appl., 7, 225
  33. Boehm A. M., 2007, BMC Bioinf., 8, 214, 10.1186/1471-2105-8-214 · DOI
  34. Pachl F., 2013, Proteomics, 13, 2552, 10.1002/pmic.201300076 · DOI
  35. Ulbrich A., 2014, J. Am. Soc. Mass Spectrom., 25, 6, 10.1007/s13361-013-0765-z · DOI

Cited by

Metadata

Authors
Werner, T., Sweetman, G., Savitski, M. F., Mathieson, T., Bantscheff, M., & Savitski, M. M.
Venue
Analytical Chemistry
Publisher
American Chemical Society (ACS)
Published
2014-03-11
Volume
86
Issue
7
Pages
3594-3601
ISSN
  • 0003-2700 (ISSN-L)
  • 1520-6882
DOI
10.1021/ac500140s
OpenAlex
W2315534050
Cited by
258
References
8
FWCI
8.43
Type
journal article
Language
en
Open access
closed

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

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.