Peptide sequence analysis using a combination of gas-phase ion͞ion chemistry and tandem mass spectrometry (MS͞MS) is demonstrated. Singly charged anthracene anions transfer an electron to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways that are analogous to those observed in electron capture dissociation. Modifications to the QLT that enable this ion͞ion chemistry are presented, and automated acquisition of high-quality, single-scan electron transfer dissociation MS͞MS spectra of phosphopeptides separated by nanoflow HPLC is described.electron capture dissociation ͉ fragmentation ͉ ion͞ion reactions ͉ charge transfer ͉ ion trap S ix years ago, McLafferty and coworkers (1) introduced a unique method for peptide͞protein ion fragmentation: electron capture dissociation (ECD). In this method, multiply protonated peptides or proteins are confined in the Penning trap of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer and exposed to electrons with near-thermal energies. Capture of a thermal electron by a protonated peptide is exothermic by Ϸ6 eV (1 eV ϭ 1.602 ϫ 10 Ϫ19 J) and causes the peptide backbone to fragment by a nonergodic process, e.g., one that does not involve intramolecular vibrational energy redistribution (2-5). One pathway for this process involves generation of an odd-electron hypervalent species (RNH 3 • ) that dissociates to produce RNH 2 and a hydrogen radical (6). As shown in Fig to an amide nitrogen, a secondary pathway, leads to the formation of carbon monoxide plus a homologous series of complementary fragment ions of types a and y. Subtraction of the m͞z values for the fragments within a given ion series that differ by a single amino acid affords the mass and thus the identity of the extra residue in the larger of the two fragments. The complete amino acid sequence of a peptide is deduced by extending this process to all homologous pairs of fragments within a particular ion series.Because ECD occurs along the peptide backbone in a sequence-independent manner, preserves posttranslational modifications (PTMs) (7-14), and can be implemented on a millisecond time scale with precursor-to-product ion conversion efficiencies that approach 30% (15-21), it has become the technique of choice for the analysis of peptide and proteins with FTICR mass spectrometers (22-28). Unfortunately, ECD in its most efficient form requires that the precursor sample ions be immersed in a dense population of near-thermal electrons. Emulating these conditions in the instruments used most commonly for peptide and protein analyses, those that trap ions with radio frequency (RF) electrostatic fields rather than with static magnetic and electric fields, remains technically challenging. Thermal electrons introduced into the RF fields of RF 3D quadrupole ion trap (QIT), quadrupole time-of-flight, or RF linear 2D quadrupole ion trap (QLT) instruments maintain their thermal energy only for a fraction of a micros...

The use of a linear or two-dimensional (2-D) quadrupole ion trap as a high performance mass spectrometer is demonstrated. Mass analysis is performed by ejecting ions out a slot in one of the rods using the mass selective instability mode of operation. Resonance ejection and excitation are utilized to enhance mass analysis and to allow isolation and activation of ions for MS n capability. Improved trapping efficiency and increased ion capacity are observed relative to a three-dimensional (3-D) ion trap with similar mass range. Mass resolution comparable to 3-D traps is readily achieved, including high resolution at slower scan rates, although adequate mechanical tolerance of the trap structure is a requirement. [8 -11], and standard three-dimensional (3-D) ion trap mass spectrometers [12,13]. Several of the quadrupole based 2-D ion traps are capable of mass selective isolation and activation of ions including MS 3 analysis [7,9 -11]. Syka and Fies have described the theoretical advantages of 2-D versus 3-D quadrupole ion traps for Fourier transform mass spectrometry [14]. These advantages include reduced space charge effects due to the increased ion storage volume, and enhanced sensitivity for externally injected ions due to higher trapping efficiencies. Bier and Syka described several forms of linear and circular 2-D ion traps with larger ion capacity to be used as mass spectrometers [15] using the mass selective instability mode of operation [16] similar to that used in all commercial 3-D quadrupole ion trap instruments.Despite the previously described advantages and the recent progress with 2-D ion traps in hybrid instruments, only a few examples have appeared using these traps as stand-alone mass spectrometers. Senko et al. recently demonstrated image current detection with FT analysis in a 2-D ion trap which utilized independent detection electrodes between the quadrupole rods [17]. Although promising results were presented, space charge effects were found to limit this configuration's ultimate performance as the motion of the ions is largely restricted to one of the symmetry planes of the device. The relative insensitivity of the image current ion detection scheme precluded the use of lower numbers of trapped ions to avoid such space charge effects.Welling et al. demonstrated two variations of mass selective instability in a stand-alone 2-D quadrupole ion trap [18]. The first method, referred to as "q-scanning", exploited the field penetration of the detector between the quadrupole rods to allow for ion extraction using a downward ramp of the RF voltage. This allowed relatively quick scanning of a broad mass range (1 second scan from 20 -1000 m/z), but produced mass spectral resolution of only five to six. The second method, referred to as "secular scanning", used frequency swept parametric excitation to eject ions between the quadrupole rods. Although the scan rate was 100x slower than the q-scan, a resolution of 800 at m/z 130 was obtained.Lammert et al. have presented preliminary results using a toroida...

We present a strategy for the analysis of the yeast phosphoproteome that uses endo-Lys C as the proteolytic enzyme, immobilized metal affinity chromatography for phosphopeptide enrichment, a 90-min nanoflow-HPLC/electrospray-ionization MS/MS experiment for phosphopeptide fractionation and detection, gas phase ion/ion chemistry, electron transfer dissociation for peptide fragmentation, and the Open Mass Spectrometry Search Algorithm for phosphoprotein identification and assignment of phosphorylation sites. From a 30-g (Ϸ600 pmol) sample of total yeast protein, we identify 1,252 phosphorylation sites on 629 proteins. Identified phosphoproteins have expression levels that range from <50 to 1,200,000 copies per cell and are encoded by genes involved in a wide variety of cellular processes. We identify a consensus site that likely represents a motif for one or more uncharacterized kinases and show that yeast kinases, themselves, contain a disproportionately large number of phosphorylation sites. Detection of a pHis containing peptide from the yeast protein, Cdc10, suggests an unexpected role for histidine phosphorylation in septin biology. From diverse functional genomics data, we show that phosphoproteins have a higher number of interactions than an average protein and interact with each other more than with a random protein. They are also likely to be conserved across large evolutionary distances.yeast phosphoproteome ͉ network analysis I n an earlier study of the yeast phosphoproteome (1), we digested proteins from a whole cell lysate with trypsin, used immobilized metal-affinity chromatography (IMAC) to enrich the sample for phosphopeptides, and analyzed the resulting mixture by nano-flow HPLC interfaced to electrospray ionization tandem mass spectrometry (MS/MS). Low-energy collision-activated dissociation (CAD) was used to fragment the peptide backbone and to produce ions of types b and y (Fig. 1) required for successful sequence analysis and identification of phosphorylation sites. We detected Ͼ1,000 phosphopeptides but defined only 383 sites of phosphorylation, largely because the CAD process often promoted elimination of phosphoric acid from Ser and Thr residues without breaking the amide bonds along the peptide backbone. The resulting MS/MS spectra were essentially devoid of sequence information.To circumvent this problem, we have modified the LTQ mass spectrometer for ion/ion chemistry and now fragment both peptides (2) and intact proteins (3) by electron transfer dissociation (ETD). In this process, fluoranthene radical-anions are generated in a chemical ionization source and used as reagents to transfer an electron to a multiply charged peptide generated by electrospray ionization. This reaction is highly exothermic, reduces the peptide charge by one, and triggers fragmentation of the peptide backbone to produce a homologous series of complementary fragment ions of type c and z⅐ (Fig. 1). Subtraction of m/z values for fragments within a given ion series that differ by a single amino acid affords the mass...

Electron-transfer dissociation (ETD) delivers the unique attributes of electron capture dissociation to mass spectrometers that utilize radio frequency trapping-type devices (e.g., quadrupole ion traps). The method has generated significant interest because of its compatibility with chromatography and its ability to: (1) preserve traditionally labile post-translational modifications (PTMs) and (2) randomly cleave the backbone bonds of highly charged peptide and protein precursor ions. ETD, however, has shown limited applicability to doubly protonated peptide precursors, [M + 2H]2+, the charge and type of peptide most frequently encountered in "bottom-up" proteomics. Here we describe a supplemental collisional activation (CAD) method that targets the nondissociated (intact) electron-transfer (ET) product species ([M + 2H]+*) to improve ETD efficiency for doubly protonated peptides (ETcaD). A systematic study of supplementary activation conditions revealed that low-energy CAD of the ET product population leads to the near-exclusive generation of c- and z-type fragment ions with relatively high efficiency (77 +/- 8%). Compared to those formed directly via ETD, the fragment ions were found to comprise increased relative amounts of the odd-electron c-type ions (c+*) and the even-electron z-type ions (z+). A large-scale analysis of 755 doubly charged tryptic peptides was conducted to compare the method (ETcaD) to ion trap CAD and ETD. ETcaD produced a median sequence coverage of 89%-a significant improvement over ETD (63%) and ion trap CAD (77%).