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Abstract
Protein subcellular localization is an essential and highly regulated determinant of protein function. Major advances in mass spectrometry and imaging have allowed the development of powerful spatial proteomics approaches for determining protein localization at the whole cell scale. Here, a brief overview of current methods is presented, followed by a detailed discussion of organellar mapping through proteomic profiling. This relatively simple yet flexible approach is rapidly gaining popularity, because of its ability to capture the localizations of thousands of proteins in a single experiment. It can be used to generate high-resolution cell maps, and as a tool for monitoring protein localization dynamics. This review highlights the strengths and limitations of the approach and provides guidance to designing and interpreting profiling experiments.
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Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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Meier F, Brunner AD, Koch S, Koch H, Lubeck M, Krause M, Goedecke N, Decker J, Kosinski T, Park MA, Bache N, Hoerning O, Cox J, Räther O, Mann M. Online Parallel Accumulation-Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer. Mol Cell Proteomics 2018; 17:2534-2545. [PMID: 30385480 PMCID: PMC6283298 DOI: 10.1074/mcp.tir118.000900] [Citation(s) in RCA: 467] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Indexed: 11/06/2022] Open
Abstract
In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of 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 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 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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Affiliation(s)
- Florian Meier
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Scarlet Koch
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Heiner Koch
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Markus Lubeck
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Michael Krause
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Niels Goedecke
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Jens Decker
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Thomas Kosinski
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., Manning Road, Billerica, Massachusetts 01821
| | - Nicolai Bache
- Evosep Biosystems, Thriges Pl. 6, 5000 Odense, Denmark
| | - Ole Hoerning
- Evosep Biosystems, Thriges Pl. 6, 5000 Odense, Denmark
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Oliver Räther
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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