Code developments to improve the efficiency of automated MS/MS spectra interpretation

We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a computational approach to narrow charge states of precursor ions from nominal resolution ion-trap tandem mass spectra. The preprocessing code, 2to3, determines the charge state of the precursor ion using its mass-to-charge ratio (m/z) and fragment ions contained in the tandem mass spectrum. For each possible charge state the program calculates the expected fragment ions that account for precursor ion m/z values. If any one of the numbers is less than an empirically determined threshold value then the spectrum corresponding to that charge state is removed. If both numbers are higher than the threshold value then +2 and +3 copies of the spectrum are kept. We present the comparison of results from protein identification experiments with and without using 2 to 3. It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results. The decrease reduces computer requirements and researcher efforts for analysis of the results.     

Semiempirical MNDO/ZINDO study of linker effects on charge transfer in nitrobenzyl-substituted tetramethyl-fulvalenes

Semiempirical MNDO and ZINDO calculations have been performed to investigate the ground states of the neutral molecules and mono- and di-cations of nitrobenzyl-substituted tetramethylfulvalene (TMF), tetramethyl-tetrahydrofulvalene (TMTHF), and tetramethyl-tetrathiafulvalene (TMTTF). In particular, the effects of the linker groups on the direct charge transfer between the fulvalene and the nitrobenzyl groups have been studied. As linkers,-(CH₂)₂-, -CH₂O-,-CH₂S-, and -CO- were used. The coefficients of the highest occupied and lowest unoccupied molecular orbitals, the oscillator strengths and excited-state dipole moments for the vertical excitations from the neutral ground states, as obtained with SCI calculations, are reported. Although the dipole moments increase by 40–50 D when exciting from the HOMO localized on the fulvalene fragment to the LUMO localized on the nitrobenzyl part, all four linkers are found to be good insulators and thus, no direct optical donor to acceptor charge transfer can be observed. An alternative route, the photoinduced charge transfer process involving local excitations to form metastable intermediate states, is discussed. Due to the insulating properties of the linkers, these will then efficiently stabilize the charge transfer complex.     

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I

The electrostatic field of the large fragment of Escherichia coli DNA polymerase I (Klenow fragment) has been calculated by the finite difference procedure on a 2 A grid. The potential field is substantially negative at physiological pH (reflecting the net negative charge at this pH). The largest regions of positive potential are in the deep crevice of the C-terminal domain, which is the proposed binding site for the DNA substrate. Within the crevice, the electrostatic potential has a partly helical form. If the DNA is positioned to fulfil stereochemical requirements, then the positive potential generally follows the major groove and (to a lesser extent) the negative potential is in the minor groove. Such an arrangement could stabilize DNA configurations related by screw symmetry. The histidine residues of the Klenow fragment give the positive field of the groove a sensitivity to relatively small pH changes around neutrality. We suggest that the histidine residues could change their ionization states in response to DNA binding, and that this effect could contribute to the protein-DNA binding energy.     

Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set

In shot-gun proteomics raw tandem MS data are processed with extraction tools to produce condensed peak lists that can be uploaded to database search engines. Many extraction tools are available but to our knowledge, a systematic comparison of such tools has not yet been carried out. Using raw data containing more than 400,000 tandem MS spectra acquired using an Orbitrap Velos we compared 9 tandem MS extraction tools, freely available as well as commercial. We compared the tools with respect to number of extracted MS/MS events, fragment ion information, number of matches, precursor mass accuracies and agreement in-between tools. Processing a primary data set with 9 different tandem MS extraction tools resulted in a low overlap of identified peptides. The tools differ by assigned charge states of precursors, precursor and fragment ion masses, and we show that peptides identified very confidently using one extraction tool might not be matched when using another tool. We also found a bias towards peptides of lower charge state when extracting fragment ion data from higher resolution raw data without deconvolution. Collecting and comparing the extracted data from the same raw data allow adjusting parameters and expectations and selecting the right tool for extraction of tandem MS data.     

Charge state estimation for tandem mass spectrometry proteomics

High-throughput protein analysis by tandem mass spectrometry produces anywhere from thousands to millions of spectra that are being used for peptide and protein identifications. Though each spectrum corresponds only to one charged peptide (ion) state, repetitive database searches of multiple charge states are typically conducted since the resolution of many common mass spectrometers is not sufficient to determine the charge state. The resulting database searches are both error-prone and time-consuming. We describe a straightforward, accurate approach on charge state estimation (CHASTE). CHASTE relies on fragment ion peak distributions, and by using reliable logistic regression models, combines different measurements to improve its accuracy. CHASTE's performance has been validated on data sets, comprised of known peptide dissociation spectra, obtained by replicate analyses of our earlier developed protein standard mixture using ion trap mass spectrometers at different laboratories. CHASTE was able to reduce number of needed database searches by at least 60% and the number of redundant searches by at least 90% virtually without any informational loss. This greatly alleviates one of the major bottlenecks in high throughput peptide and protein identifications. Thresholds and parameter estimates can be tailored to specific analysis situations, pipelines, and instrumentations. CHASTE was implemented in Java GUI-based and command-line-based interfaces.     

Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry

We describe methods for mass spectrometric identification of heme-containing peptides from c-type cytochromes that contain the CXXCH (X=any amino acid) sequence motif. The heme fragment ion yielded the most abundant MS/MS peak for standard heme-containing peptides with one amino acid difference for both 2+ and 3+ peptide charge states; both sequence and charge affect the extent of heme loss. Application to Shewanella oneidenis demonstrated the utility of this approach for identifying c-type heme-containing peptides from complex proteome samples.     

Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids

Peptoids belong to a class of sequence-controlled polymers comprising of N-alkylglycine. This study focuses on using tandem mass spectrometry techniques to characterize the fragmentation patterns of a set of singly and doubly protonated peptoids consisting of one basic residue placed at different positions. The singly protonated peptoids fragment by producing predominately high-abundant C-terminal ions called Y-ions and low-abundant N-terminal ions called B-ions. Computational studies suggest that the proton affinity (PA) of the C-terminal fragments is generally higher than that of the N-terminal fragments, and the PA of the former increases as the fragments are elongated. The B-ions are likely formed upon dissociating the proton-activated amide bonds via an oxazolone structure, and the Y-ions are produced subsequently by abstracting a proton from the newly formed B-ions, which is energetically favored. The doubly protonated peptoids prefer to fragment closest to either the N- or the C-terminus and produce corresponding B/Y-ion pairs. The basic residue seems to dictate the preferred fragmentation site, which may be the result of minimizing the repulsion between the two charges. Water and terminal neutral losses are a facile process accompanying the peptoid fragmentation in both charge states. The patterns appear to be highly influenced by the location of the basic residue.     

Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Top-down proteomics, the analysis of intact proteins (instead of first digesting them to peptides), has the potential to become a powerful tool for mass spectrometric protein characterization. Requirements for extremely high mass resolution, accuracy, and ability to efficiently fragment large ions have often limited top-down analyses to custom built FT-ICR mass analyzers. Here we explore the hybrid linear ion trap (LTQ)-Orbitrap, a novel, high performance, and compact mass spectrometric analyzer, for top-down proteomics. Protein standards from 10 to 25 kDa were electrosprayed into the instrument using a nanoelectrospray chip. Resolving power of 60,000 was ample for isotope resolution of all protein charge states. We achieved absolute mass accuracies for intact proteins between 0.92 and 2.8 ppm using the "lock mass" mode of operation. Fifty femtomole of cytochrome c applied to the chip resulted in spectra with excellent signal-to-noise ratio and only low attomole sample consumption. Different protein charge states were dissociated in the LTQ, and the sensitivity of the orbitrap allowed routine, high resolution, and high mass accuracy fragment detection. This resulted in unambiguous charge state determination of fragment ions and identification of unmodified and modified proteins by database searching. Protein fragments were further isolated and fragmented in the LTQ followed by analysis of MS(3) fragments in the orbitrap, localizing modifications to part of the sequence and helping to identify the protein with these small peptide-like fragments. Given the ready availability and ease of operation of the LTQ-Orbitrap, it may have significant impact on top-down proteomics.     

Charge Photogeneration in Organic Photovoltaics: Role of Hot versus Cold Charge‐Transfer Excitons

The role of excess excitation energy on long‐range charge separation in organic donor/acceptor bulk heterojunctions (BHJs) continues to be unclear. While ultrafast spectroscopy results argue for efficient charge separation through high‐energy charge‐transfer (CT) states within the first picosecond (ps) of excitation, charge collection measurements suggest excess photon energy does not increase the current density in BHJ devices. Here, the population dynamics of charge‐separated polarons upon excitation of high‐energy polymer states and low‐energy interfacial CT states in two polymer/fullerene blends from ps to nanosecond time scales are studied. It is observed that the charge‐separation dynamics do not show significant dependence on excitation energy. These results confirm that excess exciton energy is not necessary for the effective generation of charges.     

Study of the denaturation of the N-terminal fragment of alpha-tropomyosin by NMR spectroscopy]

Heat denaturation of the CN1A fragment (11-127) of alpha-tropomyosin was studied by NMR spectroscopy. It was shown that increasing temperature makes the fragment go through some discrete states distinguished by the spectrum of tyrosine-60. Three of these states are characterized by differences in the compact surrounding of the single tyrosine. There is a definite correlation between the observed microstates of tyrosine-60 and the realized microstates of the fragment. The appearance of different states of tyrosine is suggested to be caused by a change in the structure of its environment due to denaturation of other, rather remote regions, i.e. by appreciable mutual effects of different regions of the alpha-superhelix.     

Methanol-induced conformations of myoglobin at pH 4.0

The equilibrium methanol-induced conformation changes of holomyoglobin (hMb) at pH 4.0 have been studied by circular dichroism, tryptophan fluorescence, and Soret band absorption and by electrospray ionization mass spectrometry (ESI-MS). Optical spectra show the following: (1) In 35-40% (v/v) methanol/water, the native-like secondary structure remains, the tertiary structure is lost, the heme protein interactions are decreased, and a folding intermediate is formed. (2) In 50% methanol, heme is lost from the protein, and there is a small decrease in helicity together with a loss of tertiary structure. (3) At >60% methanol, the helicity increases and the apoprotein goes into a helical denatured state. The conformations are also probed by the charge states produced in ESI-MS and by hydrogen/deuterium (H/D) exchange with mass measurement by ESI-MS. At 0-30% methanol, native hMb produces relatively low charge states (9(+)-13(+)) in ESI-MS and exchanges relatively few hydrogens. In 35-40% methanol, at which an intermediate is formed, there is a bimodal distribution of hMb ions with both low (9(+)-13(+)) and high (14(+)-23(+)) charge states and also a high charge state distribution (12(+)-26(+)) of apomyoglobin (aMb) ions. Low and high charge states of hMb and a high charge state of aMb all show the same H/D exchange rate, indicating that an unfolded hMb intermediate interconverts between folded hMb and unfolded aMb. The charge state distribution for the unfolded hMb intermediate observed here is similar to that of the recently reported transient intermediate formed during the acid denaturation of hMb. At 50% alcohol the protein produces predominantly high charge states of aMb ions and shows H/D exchange rates close to those of the acid-denatured protein. H/D exchange of the helical denatured protein at alcohol concentrations >60%, at which high charge states of aMb are produced, shows that the protein structure is more protected than at approximately 50% methanol.     

Ethanedithiol Treatment of Solution‐Processed ZnO Thin Films: Controlling the Intragap States of Electron Transporting Interlayers for Efficient and Stable Inverted Organic Photovoltaics

The surface defects of solution‐processed ZnO films lead to various intragap states. When the solution‐processed ZnO films are used as electron transport interlayers (ETLs) in inverted organic solar cells, the intragap states act as interfacial recombination centers for photogenerated charges and thereby degrade the device performance. Here, a simple passivation method based on ethanedithiol (EDT) treatment is demonstrated, which effectively removes the surface defects of the ZnO nanocrystal films by forming zinc ethanedithiolates. The passivation by EDT treatment modulates the intragap states of the ZnO films and introduces a new intragap band. When the EDT‐treated ZnO nanocrystal films are used as ETLs in inverted organic solar cells, both the power conversion efficiency and stability of the devices are improved. The control studies show that the solar cells with EDT‐treated ZnO films exhibit reduced charge recombination rates and enhanced charge extraction properties. These features are consistent with the fact that the modulation of the intragap states results in reduction of interfacial recombination as well as the improved charge selectivity and electron transport properties of the ETLs. It is further demonstrated that the EDT treatment‐based passivation method can be extended to ZnO films deposited from sol–gel precursors.     

A pH-dependent variation in alpha-helix structure of the S-peptide of ribonuclease A studied by Monte Carlo simulated annealing.

Low-energy conformations of the S-peptide fragment (20 amino acid residues long) of ribonuclease A were studied by Monte Carlo simulated annealing. The obtained lowest-energy structures have alpha-helices with different size and location, depending distinctively on the ionizing states of acidic amino acid residues. The simulation started from completely random initial conformation and was performed without any bias toward a particular structure. The most conspicuous alpha-helices arose from the simulation when both Glu 9 and Asp 14 were assumed to be electrically neutral, whereas the resulting conformations became much less helical when Asp 14 rather than Glu 9 was allowed to have a negative charge. Together with experimental evidence that the alpha-helix in the S-peptide is most stable at pH 3.8, we consider the helix formation need the carboxyl group of Asp 14 to be electrically neutral in this weakly acidic condition. In contrast, a negative charge at Asp 14 appears to function in support of a view that this residue is crucial to helix termination owing to its possibility to form a salt bridge with His 12. These results indicate that the conformation of the S-peptide depends considerably on the ionizing state of Asp 14.     

Improved sequence tag generation method for peptide identification in tandem mass spectrometry

The sequence tag-based peptide identification methods are a promising alternative to the traditional database search approach. However, a more comprehensive analysis, optimization, and comparison with established methods are necessary before these methods can gain widespread use in the proteomics community. Using the InsPecT open source code base ( Tanner et al., Anal. Chem. 2005, 77, 4626- 39 ), we present an improved sequence tag generation method that directly incorporates multicharged fragment ion peaks present in many tandem mass spectra of higher charge states. We also investigate the performance of sequence tagging under different settings using control data sets generated on five different types of mass spectrometers, as well as using a complex phosphopeptide-enriched sample. We also demonstrate that additional modeling of InsPecT search scores using a semiparametric approach incorporating the accuracy of the precursor ion mass measurement provides additional improvement in the ability to discriminate between correct and incorrect peptide identifications. The overall superior performance of the sequence tag-based peptide identification method is demonstrated by comparison with a commonly used SEQUEST/PeptideProphet approach.     

Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain

IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index.     

An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry

We have developed a tandem mass spectrometry (MS/MS) data analysis program for confirmation of sequence of chemically modified oligonucleotides. The method is based on the analysis of deconvoluted MS/MS data for fragment ions from three charge states and comparison of these data against a set of computer-generated masses from expected fragmentation patterns. The algorithm compares the experimental masses not only against the fragment set predicted for the expected sequence but also against a wider test set covering all next-neighbor position switches of the original sequence and all pairwise swaps of nucleosides, which in synthesis would result in molecules with masses within a preset mass tolerance. The algorithm is capable of identifying incorrect sequences that would not be distinguished by identity testing with electrospray ionization mass spectrometry. The method has been tested with permutations of the two 21-mer single strands of a chemically modified short interfering RNA containing 2′-O-methyl and phosphorothioate linkages. For both strands, challenge sequences were synthesized and tested with the premise that they were the original sequences. The algorithm correctly reported the locations of next-neighbor position switches and nucleoside swaps. The results confirm the approach as useful for MS/MS-based identity test methods for synthetic oligonucleotides.     

Charge state and adduct reduction in electrospray ionization-mass spectrometry using solvent vapor exposure

The benefits of lowering protein ion charge states in electrospray ionization (ESI) have attracted recent interest. We describe a simple approach to decrease protein charge states by exposure of electrospray droplets to neutral solvent vapor such as acetonitrile. The technique allows detection of weak noncovalent complexes, provides preferred charge states for tandem mass spectrometry (MS/MS) dissociation of protein complexes, and has the added benefit of reducing common adducts, such as alkali metals, without the addition of solution additives or the requirement for a secondary spray.     

Suppressing Energy Loss due to Triplet Exciton Formation in Organic Solar Cells: The Role of Chemical Structures and Molecular Packing

In the most efficient solar cells based on blends of a conjugated polymer (electron donor) and a fullerene derivative (electron acceptor),ultrafast formation of charge‐transfer (CT) electronic states at the donor‐acceptor interfaces and efficient separation of these CT states into free charges, lead to internal quantum efficiencies near 100%. However, there occur substantial energy losses due to the non‐radiative recombinations of the charges, mediated by the loweset‐energy (singlet and triplet) CT states; for example, such recombinations can lead to the formation of triplet excited electronic states on the polymer chains, which do not generate free charges. This issue remains a major factor limiting the power conversion efficiencies (PCE) of these devices. The recombination rates are, however, difficult to quantify experimentally. To shed light on these issues, here, an integrated multi‐scale theoretical approach that combines molecular dynamics simulations with quantum chemistry calculations is employed in order to establish the relationships among chemical structures, molecular packing, and non‐radiative recombination losses mediated by the lowest‐energy charge‐transfer states.     

Role of liposome on recognition and folding of oxidized and fragmented superoxide dismutase for its re-activation

The behaviors of adsorption and folding of oxidized superoxide dismutase (SOD) fragment on the liposome surface have been studied by varying the type of liposomes. The recognition of the SOD fragment by the liposome was found to be performed, depending on the membrane fluidity, surface charge density and, also, instability of the hydrogen bonds of the liposome surface. The conformational change of the SOD fragment on the liposome membrane was dependent on its adsorption although the variation of their secondary structures was observed. The SOD LIPOzyme (liposome with enzyme-like activity) with high SOD-like activity was obtained by the appropriate control of the recognition and folding of SOD fragment through the suitably-regulated interactions between the liposome and the peptide.     

Flash-induced charge separation and dark recombination in a Photosystem-II subchloroplast particle

The decay time of flash-induced absorption changes in a Photosystem-II subchloroplast fragment is very temperature sensitive down to 210 K, below which it remains constant at 1.25 ± 0.05 ms. The difference spectrum from the near-infra-red to the ultraviolet regions indicates that the monophasic decay represents charge recombination between P-680⁺ and the reduced primary acceptor. The charge recombination proceeds by electron tunneling. The P-680 concentration in the TSF-IIa fragment was estimated to be one in 30 ± 5 total chlorophyll molecules.