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Peptide and Protein Quantification Using Itraq with Electron Transfer Dissociation

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Peptide and Protein Quantification Using Itraq with Electron Transfer Dissociation View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Peptide and Protein Quantification Using iTRAQ with Electron Transfer Dissociation Doug Phanstiel,a Yi Zhang,c Jarrod A. Marto,c,d and Joshua J. a,bCoon a Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA b Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA c Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, USA d Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides producesc- and z˙ -type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage␣ of the N–C bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (averageϽ 10%). error Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively. (J Am Soc Mass Spectrom 2008, 19, 1255–1262) © 2008 American Society for Mass Spectrometry rotein quantification has become an importantpools (e.g., control and three treatment time points). and, in many cases, critical component of Oncemodern labeled, the four samples are combined and Pmass spectrometry-based proteomic researchpeptides are sequenced individually by tandem mass [1–9]. Over the past decade, numerous quantificationspectrometry using collision-based dissociation meth- strategies have evolved—nearly all of them rely odson the[i.e., beam-type collision-activated dissociation incorporation of stable isotopes for subsequent (CAD)mass or pulsed Q dissociation (PQD)]. Identical pep- spectrometric sorting and relative quantification[10 – tides arising from each of the four samples co-elute and 19]. Time and method of isotope integration distinguishhave equivalentm/z values. During MS/MS, however, these approaches. Whether introduced metabolicallyvibrational excitation induces cleavage of both the pep- through heavy amino acids or chemically with tidediffer- backbone and the isobaric tag. Dissociation of the entially labeled tags at the peptide or proteinbackbone level, gives rise to fragment ions characteristic of mixing of the light and heavy (e.g., control andthe treated)peptide sequence; dissociation of the tag generates peptides results in co-eluting peptide pairs with lowsubtle, mass product ions where each of the four labels but measurably, different masses[10 –12, 14 –16, .20, creates21] a uniquem/z reporter peak. Because it allows for In a clever departure from this paradigm, Pappinthe simultaneous et quantification of up to four samples, al. described the concept of amine-reactive isobariciTRAQ has become an important and powerful protein tagging [13]. Here, differentially isotopically labeled quantificationbut methodology. isobaric amine-reactive tags (up to four) are embeddedDue to the loss of low mass ions during resonant into peptides from as many as four separate excitationpeptide (low mass cutoff), the use of iTRAQ labeling in conjunction with ion trap and ion trap hybrid mass spectrometers has been limited. That is, ion trap CAD Address reprint requests to Dr. J. J. Coon, Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin, 1101 University Ave, often results in the inability to detect iTRAQ reporter Madison, WI 53706, USA. E-mail: [email protected] ions due to the loss of low mass ions during precursor Published online June 17, 2008 © 2008 American Society for Mass Spectrometry. Published by Elsevier Inc. Received April 23, 2008 1044-0305/08/$32.00 Revised May 26, 2008 doi:10.1016/j.jasms.2008.05.023 Accepted May 26, 2008 1256 PHANSTIEL ET AL. J Am Soc Mass Spectrom 2008, 19, 1255–1262 fragmentation [22]. However, the rapid scanning, excel- to the manufacturer supplied protocol in ϳ70% ethanol lent sensitivity, and ability to couple with other analyz- and 0.15 M triethylammonium bicarbonate at room ers such as the orbitrap and Fourier transform ion temperature for 1 h. Samples were subsequently mixed, cyclotron resonance (FT-ICR) have made ion traps desalted using solid-phase extraction, dried to comple- among the most useful devices for protein and peptide tion, and resuspended in 100 mM acetic acid before identification [23]. Beam-type CAD is now available on LC-MS/MS analysis. hybrid ion trap-orbitrap mass spectrometers, but these systems only permit detection of product ions in the orbitrap mass analyzer, which is inherently slower and Liquid Chromatography and Mass Spectrometry less sensitive that ion trap mass analysis [24]. PQD, a form of ion trap CAD designed to eliminate low mass Synthetic peptides were resuspended in 30% acetoni- cutoff, does allow for detection of low mass-to-charge trile with 100 mM acetic acid and infused in the mass fragment ions and is available on a some ion trap and spectrometer via static nanospray Econotips (New Ob- ion trap hybrid mass spectrometers [25]. Griffin et al. jective, Woburn, MA). The six protein digest was sep- have demonstrated that PQD is compatible with iTRAQ arated on-line using nanoflow reversed-phase high- labeling and have characterized the quantitative merits performance liquid chromatography (nRP-HPLC) as of this approach [26, 27]. previously described [38]. Briefly, the sample was ϫ ␮ Electron transfer dissociation is complementary to bomb-loaded ontoa5cm 75 m i.d. precolumn ␮ CAD and can be especially useful for sequencing pep- packed with 5 m C18 reversed-phase packing material tides containing post-translational modification (PTM) (Alltech, Nicholasville, KY). This precolumn was then [28–36]. ETD allows for rapid peptide sequencing, with butt-connected toa7cmϫ 50 ␮m i.d. analytical column speeds similar to ion trap CAD, but is operated such with Teflon tubing. The sample was eluted into the that ions of mass lower than 100 m/z are detected mass spectrometer using a 60 min linear gradient from regardless of precursor m/z (i.e., no low mass cut-off). 100 mM acetic acid to 100 mM acetic acid 70% acetoni- Work by us and others demonstrate that ion trap CAD trile at a flow rate of ϳ60 nL/min. and ETD are complementary; however, ETD and other ETD reactions and mass analysis were carried out in electron-based dissociation methods rely on free radical- a hybrid linear ion trap-orbitrap mass spectrometer initiated peptide backbone cleavage and hence are not (Orbitrap; Thermo Fisher Scientific, Bremen, Germany), obviously compatible with the iTRAQ tagging strategy. which was modified as previously described to perform Here we demonstrate that ETD produces iTRAQ re- ETD reactions [39]. A negative chemical ionization porter ions, unique from those produced by CAD, and (NCI) source was fitted to the back of the instrument that these reporters allow for peptide quantification of and connected to the back of the C-trap via a multipole. up to three different samples. Fragmentation of iTRAQ The linear ion trap was modified to enable charge-sign labeled peptides with ETD results in c- and z˙-type independent trapping (CSIT). Radical fluoranthene ions fragment ions and two fragment ions resulting from are generated in the NCI source and transported down cleavage of the iTRAQ tag. One of the cleavages results the added multipole, through the C-trap and second in reporter ions that allow for quantitative comparison multipole, and finally into the linear ion trap where of up to three different samples. Synthetic peptides as ETD reactions proceed exactly as they would in a well as digests of protein standards were used to commercially available linear ion trap mass spectrom- evaluate the quality of iTRAQ based quantification in eter. After fragmentation, product ions can either be conjunction with ETD in an ETD enabled hybrid linear analyzed by the linear ion trap or sent to the orbitrap ion trap-orbitrap mass spectrometer. Peptide and pro- mass analyzer for high mass accuracy detection. All tein quantification was compared using ETD, PQD, and ETD reactions were performed for 85 ms. Precursor beam-type CAD (HCD). cation target values of 40,000 for ion trap mass analysis and 300,000
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