Abstract
Sequential Window Acquisition of all THeoretical fragment-ion (SWATH) is a recently developed discovery proteomics technique based on Data-Independent Acquisition (DIA) mass spectrometry. In this approach, MS/MS is performed simultaneously on all peptides contained in a predefined wide-open mass window of up to 25 Da. The mass window is sequentially stepped through over the entire mass range, usually between 400 and 1200 Da that covers most peptides. As quantitative MS/MS information is generated for all observable peptides in the sample, the missing data and variability between replicates are substantially reduced when compared to a Data-Dependent Acquisition approach. To identify each peptide from the high complexity of the MS/MS spectra generated from multiple peptides, a comprehensive reference spectral library derived prior from a similar sample by Data-Dependent Acquisition, rather than a conventional genome-wide database, should be used.
In this chapter, we describe a general protocol that benefits from the advances of SWATH-MS for the quantification of the primary neuronal culture proteome.
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References
Dieterich DC, Kreutz MR (2016) Proteomics of the synapse—a quantitative approach to neuronal plasticity. Mol Cell Proteomics 15(2):368–381
Pandya NJ, Koopmans F, Slotman JA, Paliukhovich I, Houtsmuller AB, Smit AB, Li KW (2017) Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution. Sci Rep 7(1):1–11
Michalski A, Cox J, Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is Inaccessible to data-dependent LC−MS/MS. J Proteome Res 10(4):1785–1793
Law KP, Lim YP (2013) Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 10(6):551–566
Koopmans F, Ho JTC, Smit AB, Li KW (2017) Comparative analyses of data independent acquisition mass spectrometric approaches: DIA, WiSIM-DIA and untargeted DIA. Proteomics 18:1700304
Bruderer R, Bernhardt OM, Gandhi T, Reiter L (2016) High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics 16(15–16):2246–2256
Wang J, Tucholska M, Knight JDR, Lambert J-P, Tate S, Larsen B, Gingras A-C, Bandeira N (2015) MSPLIT-DIA: sensitive peptide identification for data-independent acquisition. Nat Methods 12(12):1106–1108
Tsou C-C, Tsai C-F, Teo GC, Chen Y-J, Nesvizhskii AI (2016) Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers. Proteomics 16(15–16):2257–2271
Li Y, Zhong C-Q, Xu X, Cai S, Wu X, Zhang Y, Chen J, Shi J, Lin S, Han J (2015) Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files. Nat Methods 12(12):1105–1106
Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng L-Y, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, Vitek O, Rinner O, Reiter L (2015) Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Mol Cell Proteomics 14(5):1400–1410
Bruderer R, Sondermann J, Tsou C-C, Barrantes-Freer A, Stadelmann C, Nesvizhskii AI, Schmidt M, Reiter L, Gomez-Varela D (2017) New targeted approaches for the quantification of data-independent acquisition mass spectrometry. Proteomics 17(9):1700021
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227(5259):680–685
Gonzalez-Lozano MA, Klemmer P, Gebuis T, Hassan C, van Nierop P, van Kesteren RE, Smit AB, Li KW (2016) Dynamics of the mouse brain cortical synaptic proteome during postnatal brain development. Sci Rep 6(1):35456
Mineki R, Taka H, Fujimura T, Kikkawa M, Shindo N, Murayama K (2002) In situ alkylation with acrylamide for identification of cysteinyl residues in proteins during one- and two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Proteomics 2(12):1672–1681
Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11(6):O111.016717
Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD (2018) Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. Nat Methods 15(5):371–378
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372
Ladner CL, Yang J, Turner RJ, Edwards RA (2004) Visible fluorescent detection of proteins in polyacrylamide gels without staining. Anal Biochem 326(1):13–20
Escher C, Reiter L, Maclean B, Ossola R, Herzog F, Maccoss MJ, Rinner O (2014) Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12(8):1111–1121
Kang Y, Burton L, Lau A, Tate S (2017) SWATH-ID: An instrument method which combines identification and quantification in a single analysis. Proteomics 17(10):1500522
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Gonzalez-Lozano, M.A., Koopmans, F. (2019). Data-Independent Acquisition (SWATH) Mass Spectrometry Analysis of Protein Content in Primary Neuronal Cultures. In: Li, K. (eds) Neuroproteomics. Neuromethods, vol 146. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9662-9_11
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DOI: https://doi.org/10.1007/978-1-4939-9662-9_11
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