1
|
Potel CM, Lemeer S, Heck AJR. Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update. Anal Chem 2018; 91:126-141. [PMID: 30457327 PMCID: PMC6322148 DOI: 10.1021/acs.analchem.8b04746] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clement M Potel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| |
Collapse
|
2
|
Borotto NB, Ileka KM, Tom CATMB, Martin BR, Håkansson K. Free Radical Initiated Peptide Sequencing for Direct Site Localization of Sulfation and Phosphorylation with Negative Ion Mode Mass Spectrometry. Anal Chem 2018; 90:9682-9686. [PMID: 30063332 DOI: 10.1021/acs.analchem.8b02707] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tandem mass spectrometry (MS/MS) is the primary method for discovering, identifying, and localizing post-translational modifications (PTMs) in proteins. However, conventional positive ion mode collision induced dissociation (CID)-based MS/MS often fails to yield site-specific information for labile and acidic modifications due to low ionization efficiency in positive ion mode and/or preferential PTM loss. While a number of alternative methods have been developed to address this issue, most require specialized instrumentation or indirect detection. In this work, we present an amine-reactive TEMPO-based free radical initiated peptide sequencing (FRIPS) approach for negative ion mode analysis of phosphorylated and sulfated peptides. FRIPS-based fragmentation generates sequence informative ions for both phosphorylated and sulfated peptides with no significant PTM loss. Furthermore, FRIPS is compared to positive ion mode CID, electron transfer dissociation (ETD), as well as negative ion mode electron capture dissociation (niECD) and CID, both in terms of sequence coverage and fragmentation efficiency for phospho- and sulfo-peptides. Because FRIPS-based fragmentation has no particular instrumentation requirements and shows limited PTM loss, we propose this approach as a promising alternative to current techniques for analysis of labile and acidic PTMs.
Collapse
Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Kevin M Ileka
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Christina A T M B Tom
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brent R Martin
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Kristina Håkansson
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| |
Collapse
|
3
|
Quick MM, Mehaffey MR, Johns RW, Parker WR, Brodbelt JS. SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1462-1472. [PMID: 28315237 DOI: 10.1007/s13361-017-1650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
N-terminal derivatization of peptides with the chromogenic reagent 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards C-terminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LC-MS/MS workflow with 266 nm UVPD. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- M Montana Quick
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Robert W Johns
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | | |
Collapse
|
4
|
Li P, Hoffmann WD, Jackson GP. Multistage Mass Spectrometry of Phospholipids using Collision-Induced Dissociation (CID) and Metastable Atom-Activated Dissociation (MAD). INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2016; 403:1-7. [PMID: 27547107 PMCID: PMC4987003 DOI: 10.1016/j.ijms.2016.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We herein demonstrate an approach to gas phase ion manipulation that provides MS3-level CID spectra of phospholipid radical cations that are almost independent of the original charging adduct ions. In the MS2 He-MAD spectra of the protonated, sodiated and potassiated adducts of POPC, the different adducts induce different primary fragmentation pathways and provide significantly different spectra, as is commonly observed by other activation methods. In separate experiments, the even-electron adduct ions ([M+H]+, [M+Na]+, [M+K]+) of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) were first converted to radical cations [POPC]+• by using helium metastable atom-activated dissociation (He-MAD) to eject the charging adduct ions, then exposed to low-energy collision induced dissociation (CID) to induce extensive fragmentation along the acyl chains. Such charge-remote fragmentation is generally inaccessible through low-energy CID of the even-electron precursor ions. The combination of He-MAD and CID provides radical-induced spectra that show very major similarities and only minor differences, and therefore overcomes major differences in chemistry that are otherwise observed by the original adducting species. Collisional activation of even-electron [POPC+H]+ required higher CID amplitudes than odd-electron [POPC]+• to effect fragmentation-as expected-and the latter provided fragments within the acyl chains that were influenced by the double bond position.
Collapse
Affiliation(s)
- Pengfei Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - William D. Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV 26506-6121, USA
| | - Glen P. Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV 26506-6121, USA
| |
Collapse
|
5
|
Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
6
|
Deimler RE, Sander M, Jackson GP. RADICAL-INDUCED FRAGMENTATION OF PHOSPHOLIPID CATIONS USING METASTABLE ATOM-ACTIVATED DISSOCIATION MASS SPECTROMETRY (MAD-MS). INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:178-186. [PMID: 26644782 PMCID: PMC4669893 DOI: 10.1016/j.ijms.2015.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The fragmentation pattern of several protonated 1+ phosphatidylcholines (PCs) were studied using low energy collision induced dissociation (CID) and helium metastable atom-activated dissociation (He-MAD). He-MAD of the protonated compounds produced a dominant phosphocholine head group at m/z 184 as well as typical sn-1 and sn-2 glycerol fragments such as [M+H-Rx-1CHC=O]+ and [M+H-Rx-1CO2H]+. Within the aliphatic chain, He-MAD showed fragments consistent with high-energy collision induced dissociation (HE-CID) and products/pathways consistent with Penning ionization of the 1+ precursor ions to their respective radical dications. These Penning ionization products included both singly and doubly charged radical fragments, and the fragment ions are related to the number and position of double bonds in the acyl chains. Fragments created through HE-CID-like fragmentation followed classic charge remote fragmentation pathways including ladder-like fragmentation along the acyl chain, except for additional or missing peaks due to predictable rearrangement reactions. He-MAD therefore shows utility in being able to effectively fragment singly charged lipids into a variety of useful product ions using both radical and high-energy processes in the confines of a 3D ion trap.
Collapse
Affiliation(s)
- Robert E. Deimler
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | | | - Glen P. Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506
- Department of Forensic & Investigative Science, West Virginia University, Morgantown, WV, 26506-6121
- Corresponding Author. Correspondence to: Glen P. Jackson, , 305-293-9236
| |
Collapse
|
7
|
Donohoe GC, Khakinejad M, Valentine SJ. Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:564-576. [PMID: 25510931 DOI: 10.1007/s13361-014-1045-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.
Collapse
Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | | |
Collapse
|
8
|
Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry. Anal Chim Acta 2015; 854:106-17. [DOI: 10.1016/j.aca.2014.10.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/14/2022]
|
9
|
Hoffmann WD, Jackson GP. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1939-43. [PMID: 25231159 DOI: 10.1007/s13361-014-0989-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
Collapse
Affiliation(s)
- William D Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506, USA
| | | |
Collapse
|