The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Multiplexed peptide analysis using data-independent acquisition and Skyline
Open accessAbstract
Here we describe the use of data-independent acquisition (DIA) on a Q-Exactive mass spectrometer for the detection and quantification of peptides in complex mixtures using the Skyline Targeted Proteomics Environment (freely available online at http://skyline.maccosslab.org). The systematic acquisition of mass spectrometry (MS) or tandem MS (MS/MS) spectra by DIA is in contrast to DDA, in which the acquired MS/MS spectra are only suitable for the identification of a stochastically sampled set of peptides. Similarly to selected reaction monitoring (SRM), peptides can be quantified from DIA data using targeted chromatogram extraction. Unlike SRM, data acquisition is not constrained to a predetermined set of target peptides. In this protocol, a spectral library is generated using data-dependent acquisition (DDA), and chromatograms are extracted from the DIA data for all peptides in the library. As in SRM, quantification using DIA data is based on the area under the curve of extracted MS/MS chromatograms. In addition, a quality control (QC) method suitable for DIA based on targeted MS/MS acquisition is detailed. Not including time spent acquiring data, and time for database searching, the procedure takes ∼1–2 h to complete. Typically, data acquisition requires roughly 1–4 h per sample, and a database search will take 0.5–2 h to complete.
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Cites
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq054 · Cited by 4,697
Self-citationAnderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414
Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Self-citationRapid empirical discovery of optimal peptides for targeted proteomics
Stergachis, A. B., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J. (2011) · Nature Methods · doi:10.1038/nmeth.1770 · Cited by 110
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Basisty, N., Kale, A., Jeon, O. H., Kuehnemann, C., Payne, T., Rao, C., Holtz, A., Shah, S., Sharma, V., Ferrucci, L., et al. (2020) · PLOS Biology · doi:10.1371/journal.pbio.3000599 · Cited by 1,348
Targeted delivery of a PD-1-blocking scFv by CAR-T cells enhances anti-tumor efficacy in vivo
Rafiq, S., Yeku, O. O., Jackson, H. J., Purdon, T. J., van Leeuwen, D. G., Drakes, D. J., Song, M., Miele, M. M., Li, Z., Wang, P., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4195 · Cited by 833
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
Pino, L. K., Searle, B. C., Bollinger, J. G., Nunn, B., MacLean, B., & MacCoss, M. J. (2020) · Mass Spectrometry Reviews · doi:10.1002/mas.21540 · Cited by 800
Self-citationSearle, B. C., Pino, L. K., Egertson, J. D., Ting, Y. S., Lawrence, R. T., MacLean, B. X., Villén, J., & MacCoss, M. J. (2018) · Nature Communications · doi:10.1038/s41467-018-07454-w · Cited by 522
Self-citationSelective degradation of splicing factor CAPERα by anticancer sulfonamides
Uehara, T., Minoshima, Y., Sagane, K., Sugi, N. H., Mitsuhashi, K. O., Yamamoto, N., Kamiyama, H., Takahashi, K., Kotake, Y., Uesugi, M., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2363 · Cited by 396
Metadata
- Authors
- Egertson, J. D., MacLean, B., Johnson, R., Xuan, Y., & MacCoss, M. J.
- Venue
- Nature Protocols
- Published
- 2015-05-21
- Volume
- 10
- Issue
- 6
- Pages
- 887-903
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W1541396877
- Cited by
- 211
- References
- 6
- FWCI
- 10.19
- Type
- journal article
- Language
- en
- Open access
- green
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