Does the mass spectrometer define the marker? A comparison of global metabolite profiling data generated simultaneously via UPLC-MS on two different mass spectrometers
Open accessAbstract
By coupling a single UPLC separation to two different types of mass spectrometer an unbiased comparison of the metabolite profiles produced by each instrument for a set of rat urine samples was obtained. The flow from the UPLC column was split equally and both streams of eluent were simultaneously directed to the inlets of the two mass spectrometers. Mass spectrometry on the eluent was undertaken using a triple quadrupole linear ion trap and a hybrid quadrupole time-of-flight mass spectrometer using both positive and negative ESI. Data from both mass spectrometers were subjected to multivariate statistical analysis, after applying the same data extraction software, and showed the same general pattern of correlation between the samples using both unsupervised and supervised methods of statistical analysis. Based on orthogonal partial least-squares discriminant analysis models a number of ions were recognized as "responsible" for the separation of the animal groups. From the peaks detected, and denoted as significant by the statistical analysis a number of ions were found to be unique to one data set or the other, a result which may have consequences for biomarker discovery and interlaboratory comparisons. The software package used for data analysis also had an effect on the outcome of the statistical analysis.
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.
Integrity signals
Registry
Cites
Statistics
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Variables affecting the final data set include sample preparation mode, chromatography method, detection mode, and choice of data reduction methods.
“These include the mode of sample preparation, method of chromatography, mode of detection, and the choice of data reduction methods (116, 117).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [117]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. A., & Siuzdak, G. E. (2006) · Analytical Chemistry · doi:10.1021/ac051437y · Cited by 5,296 · see citing works
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., & Siuzdak, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812874106 · Cited by 2,677 · see citing works
Data processing for mass spectrometry-based metabolomics
Katajamaa, M., & Orešič, M. (2007) · Journal of Chromatography A · doi:10.1016/j.chroma.2007.04.021 · Cited by 616 · see citing works
Analytical Strategies in Metabonomics
Lenz, E. M., & Wilson, I. D. (2006) · Journal of Proteome Research · doi:10.1021/pr0605217 · Cited by 530 · see citing works
Self-citationGika, H., Theodoridis, G. A., Wingate, J. E., & Wilson, I. D. (2007) · Journal of Proteome Research · doi:10.1021/pr070183p · Cited by 502 · see citing works
Self-citationWilson, I. D., Nicholson, J. K., Castro‐Perez, J. M., Granger, J. H., Johnson, K. A., Smith, B. W., & Plumb, R. S. (2005) · Journal of Proteome Research · doi:10.1021/pr049769r · Cited by 421 · see citing works
Self-citationLC-MS-based methodology for global metabolite profiling in metabonomics/metabolomics
Theodoridis, G., Gika, H. G., & Wilson, I. D. (2008) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2008.01.008 · Cited by 371 · see citing works
Self-citationGika, H., Macpherson, E., Theodoridis, G. A., et al. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.05.048 · Cited by 231 · see citing works
Self-citationShen, Y., Zhang, R., Moore, R. J., Kim, J., Metz, T., Hixson, K. K., Zhao, R., Livesay, E. A., Udseth, H. R., & Smith, R. D. (2005) · Analytical Chemistry · doi:10.1021/ac0483062 · Cited by 230 · see citing works
Theodoridis, G. A., Gika, H., & Wilson, I. D. (2011) · Mass Spectrometry Reviews · doi:10.1002/mas.20306 · Cited by 218 · see citing works
Self-citationPlumb, R. S., Stumpf, C. L., Gorenstein, M. V., Castro‐Perez, J. M., Dear, G. J., Anthony, M. L., Sweatman, B. C., Connor, S. C., & Haselden, J. N. (2002) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.813 · Cited by 216 · see citing works
LC–MS-based metabonomics analysis
Lu, X., Zhao, X., Bai, C., Zhao, C., Guo, L., & Xu, G. (2007) · Journal of Chromatography B · doi:10.1016/j.jchromb.2007.10.022 · Cited by 195 · see citing works
Yin, P., Zhao, X., Li, Q., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr060256p · Cited by 151 · see citing works
Lenz, E. M., Bright, J. D., Knight, R., Westwood, F. R., Davies, D. T., Major, H. J., & Wilson, I. D. (2005) · Biomarkers · doi:10.1080/13547500500094034 · Cited by 130 · see citing works
Self-citationWilliams, R. E., Lenz, E. M., Lowden, J. S., Rantalainen, M., & Wilson, I. D. (2005) · Molecular BioSystems · doi:10.1039/b500852b · Cited by 115 · see citing works
Self-citationLafaye, A., Junot, C., Gall, B. R., et al. (2003) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1243 · Cited by 94 · see citing works
SUMNER, S. S., Burgess, J. P., Snyder, R. W., et al. (2010) · Metabolomics · doi:10.1007/s11306-010-0197-8 · Cited by 36 · see citing works
Self-citationA Statistically Rigorous Test for the Identification of Parent−Fragment Pairs in LC-MS Datasets
Ipsen, A. B., Want, E. J., Lindon, J. C., et al. (2010) · Analytical Chemistry · doi:10.1021/ac902361f · Cited by 33 · see citing works
Verpoorte, R., Choi, Y. H., & Kim, H. K. (2009) · Phytochemical Analysis · doi:10.1002/pca.1191 · Cited by 28 · see citing works
Pandher, R., Ducruix, C., Eccles, S. A., & Raynaud, F. I. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.12.001 · Cited by 27 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The food metabolome: a window over dietary exposure
Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.076133 · Cited by 519 · see citing works
- Authors
- Gika, H. G., Theodoridis, G. A., Earll, M., Snyder, R. W., Sumner, S. J., & Wilson, I. D.
- Affiliations
- RTI International (US)
- Corresponding author
- Theodoridis, Georgios A.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-09-09
- Volume
- 82
- Issue
- 19
- Pages
- 8226-8234
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC2951889
- OpenAlex
- W1980053022
- Cited by
- 61
- References
- 20
- Citations by year
- 2026: 1 · 2025: 3 · 2023: 2 · 2022: 3 · 2021: 1 · 2020: 4 · 2019: 3 · 2018: 3 · 2017: 5 · 2016: 6 · 2015: 2 · 2014: 7 · 2013: 9 · 2012: 6
- FWCI
- 2.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (5R21GM75903, R21GM075903)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- UPLC-MS, rat urine, biomarker discovery, interlaboratory comparison, OPLS-DA, data extraction software
- MeSH terms
- Animals, Chromatography, High Pressure Liquid, Isoniazid, Models, Statistical, Biomarkers, Spectrometry, Mass, Electrospray Ionization, Principal Component Analysis, Rats, Metabolome
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
