Review
doi: 10.1021/acs.analchem.5b04563. Epub 2015 Dec 11.Ion Activation Methods for Peptides and Proteins
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- PMID:26630359
- PMCID: PMC5553572
- DOI: 10.1021/acs.analchem.5b04563
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Review
Ion Activation Methods for Peptides and Proteins
Jennifer S Brodbelt. Anal Chem..
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Conflict of interest statement
The authors declare no competing financial interest.
Figures
Concept of bottom-up, middle-down, and top-down proteomic strategies.
Types of fragment ions produced for peptides and proteins.
Comparison of conventional and multiplex methods for MS/MS data acquisition. Adapted from: Multiplexed and data-independent tandem mass spectrometry for global proteome profiling, Chapman, J.D., Goodlett, D.R., Masselon, C.D.Mass Spectrom. Rev.2014, Vol. 33, 452–470 (ref. 167). Copyright 2014 Wiley.
Examples of peptide fragmentation by A) ETD, B) ETcaD, C) HCD, and D) EThcD for peptide EGVNDNEEGFFSAR. Reproduced from Frese, C.K., Altelaar, A.F.M.,van den Toorn, H., Nolting, D., Griep-Raming, J., Heck, A.J.R., Mohammed, S.,Anal. Chem.,2012, 84, 9668–9673 (ref 194). Copyright 2012 American Chemical Society.
Schematic of Orbitrap mass spectrometer equipped with laser for photodissociation and examples of UVPD mass spectra of the 11+ charge state of (A) ubiquitin and (B) the 20+ charge state of myoglobin. Reproduced from Shaw, J.B., Li, W., Holden, D.D., Zhang, Y., Griep-Raming, J., Fellers, R.T., Early, B.P., Thomas, P.M., Kelleher, N.L., Brodbelt, J.S.J. Am. Chem. Soc.,2013, 135, 12646–12651 (ref 116). Copyright 2013 American Chemical Society.
Nano-electrospray SID (middle panel) and CID (right panel) mass spectra of the charge-reduced +11 precursor of (B and C) SA, (E and F) neutravidin, and (H and I) TTR at three separate collision energies. All fragments are labeled based on their corresponding peaks detected in IM. The precursor ion in each spectrum is indicated by a purple asterisk. Crystal structures of (A) SA (PDB: 1SWB), (D) neutravidin (PDB: 1VYO), and (G) TTR (PDB: 1F41) are shown in the left panel. Subunits I, II, III, and IV are also shown in blue, green, yellow, and red, respectively. Reproduced fromChemistry & Biology, Vol. 22, Quintyn, Q., Yan, J., Wysocki, V.H., Surface-Induced Dissociation of Homotetramers with D2 Symmetry Yields their Assembly Pathways and Characterizes the Effect of Ligand Binding, pp. 583–592, Copyright (2015), (ref. 142) with permission from Elsevier.
Broadband isolation of the antibody hexamer in complex with CD38 antigen molecules followed by collisional dissociation at acceleration voltages of (a) 100 V, (b) 150 V, and (c) 200 V. (d) Color annotation of fragment ions produced by collisional dissociation of the IgG1–005 hexamer:CD38 complex at 150 V colored according to the number of CD38 subunits present; the inset schematically shows suggested spatial arrangement of the subunits in the complex. As the dominant fragment ions series corresponds to an IgG:CD38 complex of 6:11, the predominant precursor ions should have been the 6:12 IgG:CD38 complex. Reproduced from Dyachenko, A., Wang, G., Belov, M., Makarov, A., de Jong, R.N., van den Bremer, E.T., Pareren, P.W.H.I., Heck, A.J.R.Anal. Chem.,2015, 87, 6095–6102 (ref 264). Copyright 2015 American Chemical Society.
Plots of TIC abundance per residue based on summed holo + apo product ions (including both N-termini and C-termini ions) from DHFR and its respective complexes DHFR●NADPH (a), DHFR●MTX (b), and DHFR●NADPH●MTX (c). The 9+ charge state was selected for all experiments. The color code used for each protein is shown in the legends. Standard deviations were calculated from four replicates. (d) Space-filled model of NADPH (in blue/red/orange spheres) and the predicted interacting residues of DHFR (purple spheres) based on UVPD fragmentation. The residues of DHFR presumed to interact with NADPH correspond to those that show overlapping N- and C-termini holo ions from backbone cleavages upon UVPD. Other holo (NADPH-containing) fragment ions from the N-terminus are highlighted in blue, and other holo (NADPH-containing) fragment ions from the C-terminus are highlighted in red (non-space filled). Reproduced from Cammarata, M.; Thyer, R., Rosenberg, J., Ellington, A., Brodbelt, J.S.J. Am. Chem. Soc.,2015, 137(28) 9128–9135 (ref 263). Copyright 2015 American Chemical Society.
GroEL mass spectra acquired under the following conditions: (A) signal obtained by trapping an intact 14-mer GroEL complex in the C-trap; (B) signal of the GroEL monomer subunit obtained upon collisional activation between the funnel exit electrode and inject flatapole. The GroEL monomer ions were accumulated in the C-trap; (C) subunit backbone-level spectrum upon 200 V collisional activation in the HCD cell; The inset shows the signal of one of the GroEL fragment ions (b63) identified at a mass measurement accuracy of 2.3 ppm. Reproduced from: Belov, M.E., Damoc, E., Denisov, E., Compton, P.D., Horning, S., Makarov, A.A., Kelleher, N.L..Anal. Chem.,2013, 85, 11163–11173 (ref 246). Copyright 2013 American Chemical Society
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