The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer
Open accessAbstract
ABSTRACT In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation – serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al. , PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 800,000 fragmentation spectra in standard 120 min LC runs are easily achievable, which can be used for near exhaustive precursor selection in complex mixtures or re-sequencing weak precursors. MaxQuant identified more than 6,400 proteins in single run HeLa analyses without matching to a library, and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,900 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.
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Citations
Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationMass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationCox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.031591 · Cited by 5,180
Self-citationRoss, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401
Mass-spectrometric exploration of proteome structure and function
Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334
Self-citationKulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719
Self-citationLanucara, F., Holman, S. W., Gray, C. J., & Eyers, C. E. (2014) · Nature Chemistry · doi:10.1038/nchem.1889 · Cited by 901
Michalski, A., Cox, J., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101060v · Cited by 685
Self-citationReview on ion mobility spectrometry. Part 1: current instrumentation
Cumeras, R., Figueras, E., Davis, C. E., Baumbach, J. I., & Gràcia, I. (2015) · The Analyst · doi:10.1039/c4an01100g · Cited by 459
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“The EvoSep system was coupled online to a trapped ion mobility spectrometry quadrupole time-of-flight mass spectrometer 57 (timsTOF Pro, Bruker Daltonik) via a nano-electrospray ion source (Captive spray, Bruker Daltonik).”
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Metadata
- Authors
- Meier, F., Brunner, A.-D., Koch, S., Koch, H., Lubeck, M., Krause, M., Goedecke, N., Decker, J., Kosinski, T., Park, M. A., Bache, N., Hoerning, O., Cox, J., Räther, O., & Mann, M.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2018-12
- Volume
- 17
- Issue
- 12
- Pages
- 2534-2545
- ISSN
- 1535-9476 (ISSN-L)
- OpenAlex
- W2952907530
- Cited by
- 965
- References
- 9
- FWCI
- 28.06
- Type
- journal article
- Language
- en
- Open access
- hybrid
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