The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Using i RT, a normalized retention time for more targeted measurement of peptides
Open accessAbstract
Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present i RT, an empirically derived dimensionless peptide‐specific value that allows for highly accurate RT prediction. The i RT of a peptide is a fixed number relative to a standard set of reference i RT‐peptides that can be transferred across laboratories and chromatographic systems. We show that i RT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. i RT s can be determined by any laboratory and shared transparently. The i RT concept has been implemented in S kyline, the most widely used software for MRM experiments.
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Cites
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574
Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037
Deep proteome and transcriptome mapping of a human cancer cell line
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979
The quantitative proteome of a human cell line
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816
Self-citationFull dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744
mProphet: automated data processing and statistical validation for large-scale SRM experiments
Reiter, L., Rinner, O., Picotti, P., Hüttenhain, R., Beck, M., Brusniak, M.-Y., Hengartner, M. O., & Aebersold, R. (2011) · Nature Methods · doi:10.1038/nmeth.1584 · Cited by 532
Self-citationKrokhin, O. V., Craig, R., Spicer, V., Ens, W., Standing, K. G., Beavis, R. C., & Wilkins, J. A. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400031-mcp200 · Cited by 284
Cited by
Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens
Gubin, M. M., Zhang, X., Schuster, H., Caron, E., Ward, J. P., Noguchi, T., Ivanova, Y., Hundal, J., Arthur, C. D., Krebber, W.-J., et al. (2014) · Nature · doi:10.1038/nature13988 · Cited by 1,974
“Retention times were extracted from the spectra and converted into a system-independent retention time (iRT) using spiked-in calibration peptides (Biognosys) 45 .”
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Shen, B., Yi, X., Sun, Y., Bi, X., Du, J., Zhang, C., Quan, S., Zhang, F., Sun, R., Qian, L., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.032 · Cited by 1,514
Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238
Self-citationTau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer’s Disease
Wesseling, H., Mair, W., Kumar, M., Schlaffner, C. N., Tang, S., Beerepoot, P., Fatou, B., Guise, A. J., Cheng, L., Takeda, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.029 · Cited by 688
“Vacuumdried peptides were reconstituted in sample buffer (5% formic acid, 5% acetonitrile (ACN)) containing indexed retention time (iRT) peptides (Biognosys) (Escher et al., 2012) and 10 fmol/μl non-labeled FLEX-peptide and 100 fmol/ul heavy-isotope labeled isoform specific peptides (AEEAGIGDTPSL[+7.”
MethodCollins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00249-5 · Cited by 576
Metadata
- Authors
- Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M. J., & Rinner, O.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2012-04
- Volume
- 12
- Issue
- 8
- Pages
- 1111-1121
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- OpenAlex
- W2039058260
- Cited by
- 600
- References
- 8
- FWCI
- 13.17
- Type
- journal article
- Language
- en
- Open access
- green
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- Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M. J., & Rinner, O. (2012). Using i RT, a normalized retention time for more targeted measurement of peptides. PROTEOMICS. https://doi.org/10.1002/pmic.201100463
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