Tissue Classification After Bone-Anchored Hearing Implant Surgery: A Machine Learning Approach to Monitoring Skin Response.

HYPOTHESIS: Here, we aim to 1) expand the available evidence for the use of machine learning techniques for soft tissue classification after BCD surgery and 2) discuss the implications of such approaches toward the development of classification applications to aid in tissue monitoring. BACKGROUND: The application of machine learning techniques in the soft tissue literature has become a large field of study. One of the most commonly reported outcomes after percutaneous bone-conduction device (BCD) surgery is soft tissue health. Unfortunately, the classification of tissue around the abutment as healthy versus not healthy is a subjective process, even though such decisions can have implications for treatment (i.e., topical steroid versus surgical revision) and resources (e.g., clinician time). METHODS: We built and tested a convolutional neural network (CNN) model for the classification of tissues that were rated as "green" (i.e., healthy), "yellow" (i.e., unhealthy minor), and "red" (i.e., unhealthy severe). METHODS: Representative image samples were gathered from a regional bone-conduction amplification site (N = 398; 181 samples of green; 144 samples of yellow; 73 samples of red). The image samples were cropped, zoomed, and normalized. Feature extraction was then implemented and used as the input to train an advanced CNN model. RESULTS: Accuracy of image classification for the healthy ("green") versus not healthy ("yellow" and "red") model was approximately 87%. Accuracy of image classification for the unhealthy ("yellow") versus unhealthy ("red") model was approximately 94%. CONCLUSIONS: Monitoring tissue health is an ongoing challenge for BCD users and their clinicians not trained in soft tissue management (e.g., audiologists). If machine learning can aid in the classification of tissue health, this would have significant implications for stakeholders. Here we discuss how machine learning can be applied to tissue classification as a potential technological aid in the coming years.

Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna-Matthews-Olson Complex Example.

Multiscale molecular modeling is utilized to predict optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular dynamics simulations with structural refinement of photosynthetic pigments and calculations of their excited states in a polarizable protein environment. The only experimental input to the modeling protocol is the X-ray structure of the wild-type protein. The first-principles modeling reproduces changes in the experimental optical spectra of the considered mutants, Y16F and Q198V. Interestingly, the Q198V mutation has a negligible effect on the electronic properties of the targeted bacteriochlorophyll a pigment. Instead, the electronic properties of several other pigments respond to this mutation. The molecular modeling demonstrates that a single-point mutation can induce long-range effects on the protein structure, while extensive structural changes near a pigment do not necessarily lead to significant changes in the electronic properties of that pigment.

Two Algorithms for Excited-State Quantum Solvers: Theory and Application to EOM-UCCSD.

Near-term quantum devices promise to revolutionize quantum chemistry, but simulations using the current noisy intermediate-scale quantum (NISQ) devices are not practical due to their high susceptibility to errors. This motivated the design of NISQ algorithms leveraging classical and quantum resources. While several developments have shown promising results for ground-state simulations, extending the algorithms to excited states remains challenging. This paper presents two cost-efficient excited-state algorithms inspired by the classical Davidson algorithm. We implemented the Davidson method into the quantum self-consistent equation-of-motion unitary coupled-cluster (q-sc-EOM-UCC) excited-state method adapted for quantum hardware. The circuit strategies for generating desired excited states are discussed, implemented, and tested. We demonstrate the performance and accuracy of the proposed algorithms (q-sc-EOM-UCC/Davidson and its variational variant) by simulations of H2, H4, LiH, and H2O molecules. Similar to the classical Davidson scheme, q-sc-EOM-UCC/Davidson algorithms are capable of targeting a small number of excited states of the desired character.

Expulsion of Hydroxide Ions from Methyl Hydration Shells.

The affinity of hydroxide ions for methyl hydration shells is assessed using a combined experimental and theoretical analysis of tert-butyl alcohol (TBA) dissolved in pure water and aqueous NaOH and NaI. The experimental results are obtained using Raman multivariate curve resolution (Raman-MCR) and a new three-component total least squares (Raman-TLS) spectral decomposition strategy used to highlight vibrational perturbations resulting from interactions between TBA and aqueous ions. The experiments are interpreted and extended with the aid of effective fragment potential molecular dynamics (EFP-MD) simulations, as well as Kirkwood-Buff calculations and octanol/water partition measurements, to relate TBA-ion distribution functions to TBA solubility changes. The combined experimental and simulation results reveal that methyl group hydration shells more strongly expel hydroxide than iodide anions, whose populations near the methyl groups of TBA are predicted to be correlated with sodium counterion localization near the TBA hydroxyl group.

Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database.

An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as "flexible EFP", is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.

Histological Analysis of Reproductive System in Low-Dose Nonylphenol-treated F1 Female Mice.

Previously, we reported adverse effects of low-dose nonylphenol (NP) exposure on the reproductive parameters of F1 female mice. In the present study we further investigated the pathohistological effect of NP exposure on the reproductive organs in F1 female mice. NP exposures were continuously conducted from parental pre-mating period until the postnatal day (PND) 33 of F1 offspring for vaginal examination. Mice were sacrificed on PND 30 and the reproductive tissue weights were measured. The initial (at PND 21) body weights of the NP-50 group animals were significantly lower than those of control group animals, and the weight deficit were recovered when the terminal (PND 33) body weights were measured. Early vaginal opening was found in NP group animals (p<0.05). Pathohistological studies revealed that NP-treated F1 animals showed prominent increase in the ovarian follicle numbers (p<0.01), and decrease in the diameter of uterine myometrium (p<0.01), and increase in the diameter of luminal epithelium (p<0.05). The present study demonstrated that the subchronic low-dose NP exposure induced early beginning of puberty and pathohistological abnormalities in ovary and uterus of F1 mice. Further studies are needed to achieve a better understanding on the action mechanism of NP in pubertal onset and to find a way to avoid a hazardous situation provoked by NP exposure.

Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex.

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.

The unusual symmetry of hexafluoro-o-xylene-A microwave spectroscopy and computational study.

The rotational constants and quartic centrifugal distortion coefficients of hexafluoro-o-xylene were precisely derived from the 8 GHz to 18 GHz gas phase microwave spectrum. In addition, the rotational constants of all singly substituted 13C isotopologues were determined. Instead of the intuitively expected symmetry of C2v, as in o-xylene, calculations with a variety of methods (B3LYP, CAM-B3LYP, ωB97XD, MP2, and coupled-cluster singles, doubles, and perturbative triples) predict a C2 symmetry structure in which the two CF3 groups rotate in opposite directions by about 16°. While the experimental results in this study are not capable of proving this unusual symmetry, they can support future microwave, gas phase electron diffraction or nuclear magnetic resonance studies. From the presented data, a preliminary r0 structure was determined, reproducing the experimental rotational constants with deviations of no more than 15 kHz. Analysis of the interactions between the two CF3 groups using an effective fragment potential approach identifies two major contributions to their interaction, due to exchange-repulsion and electrostatic repulsion, with electrostatic repulsion responsible for the barrier at the C2v geometry.

FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method.

In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.

Adverse Effect of Nonylphenol on the Reproductive System in F2 Male Mice : A Qualitative Change?

Previously, we reported negative effects of low-dose nonylphenol (NP) exposure on the reproductive organs of F1 male mice. In the present study was further investigated the endocrine disrupting effect of NP exposure to F2 generation male mice. Mice were divided into 2 groups; (1) CON, control animals and (2) NP-50 (50 µg/L), animals were treated with NP via drinking water. NP exposures were continuously conducted from parental pre-mating period until the postnatal day (PND) 55 of F2 offsprings. Mice were sacrificed on PND 55 and the reproductive tissue weights were measured. The initial (at PND 21) and terminal (PND 55) body weights of the NP-50 group animals were not significantly different from those of control group animals. NP exposure fail to induce a significant weight change of the testes, seminal vesicle and prostate except absolute epididymal weight (p<0.05). However, pathohistological studies revealed that NP-treated F2 animals showed evident decrease in seminiferous tubule diameters, reduced luminal area and number of germ cells. Also, sloughing morphologies in the tubules were notable. In the caudal epididymis, fewer mature sperms and swollen epithelial cells were found in the NP-treated group. The present study demonstrated that the subchronic low-dose NP exposure induced pathohistological abnormalities in testis and epididymis of F2 mice, and we assumed that these 'qualitative' changes in reproductive tissues could be derived from the epigenetic modifications such as DNA methylation, histone modification, altered DNA accessibility and chromatin structure. Further studies are needed to achieve a better understanding on the multi- or trans-generational effects of NP on the reproductive health and a human application.

Adverse Effect of Nonylphenol on the Reproductive System in F1 Male Mice: A Subchronic Low-Dose Exposure Model.

Nonylphenols (NPs) are widely used industrial materials, and are considered as potent endocrine disrupting chemical. Present study was undertaken to clarify the effect of subchronic low-dose NP exposure to F1 generation male mice. Mice were divided into 2 groups; (1) CON, control animals and (2) NP-50 (50 µg/L), animals were treated with NP via drinking water. NP exposures were continuously conducted from parental pre-mating period until the postnatal day (PND) 55 of F1 offsprings. Mice were sacrificed on PND 55 and the tissue weights were measured. The initial body weights (at PND 21) and terminal body weights (PND 55) of the NP-50 animals were significantly lower than those of control animals (p<0.05). NP exposure induced a significant increase in the absolute weight of the testes (p<0.05). Conversely, the NP exposure caused significant decrease in the absolute weights of the epididymis (p<0.01), prostate (p<0.05) and seminal vesicle (p<0.05). Histopathological studies revealed that NP-treated animals exerted decreased seminiferous tubule diameters, reduced luminal area, and lower number of germ cells. Also some sloughing morphologies in the tubules were observed. In the caudal epididymis, fewer mature sperms and swollen epithelial cells were found in the NP-treated group. Our results confirmed that the subchronic low-dose NP exposure altered some male parameters and induced histopathological abnormalities in testis and epididymis of F1 mice. Since the NP dose used in this study is close to the average human daily NP exposure, our results could provide practically meaningful understanding of adverse effect of EDC in human.

Polarizable embedding for simulating redox potentials of biomolecules.

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The approach is tested on simulating reduction potential of cryptochrome 1 protein from Arabidopsis thaliana. The theoretical estimate (0.07 V) of the midpoint reduction potential is in good agreement with available experimental data (-0.15 V).

Effect of High Fructose Corn Syrup (HFCS) Intake on the Female Reproductive Organs and Lipid Accumulation in Adult Rats.

High-fructose corn syrup (HFCS) is widely used as sweetener, and its overconsumption is become a major health problem. In the present study, we used adult female rats and applied a 28 days HFCS feeding model to monitor the estrous cycle and changes in tissue weights and histology. Adult female rats were divided into three groups. Animals were fed with ad libitum normal chow and (1) 24 hours tap water (Control group), (2) 12 hours HFCS access during dark period and 12 hours tap water (12H group), and (3) 24 hours HFCS only access (24H group). Total exposure period was 28 days. There is no significant change in body weight between control and HFCS-fed animals. Both absolute and relative weights of ovary in 24H animals were significantly heavier than those in control or 12H animals. The absolute and relative weights of the kidney and liver in 24H groups were significantly heavier than those in control or 12H animals. The estrous cycles of the 24H animals were significantly longer. Histological analyses revealed that 24H ovaries were relatively bigger and possessed more corpus lutea than control ovaries. Uterine sections of 12H and 24H animals showed a well-developed stratum vasculare between inner and outer myometrial layers. The number of endometrial glands were decreased in 12H uteri, and recovered in 24H uteri compared to control. Numbers of convoluted tubule in distal region increased in 12H and 24H kidney samples. Liver specimens of 12H and 24H showed the increased number of fat containing vacuoles. In conclusion, our study demonstrated that HFCS treatment for 28 days could induce (1) changes in length of estrous cycle with extended estrous and diestrous stages, (2) altered ovarian and uterine histology, and (3) liver and renal lipid accumulation. These findings reveal the adverse effects of HFCS drinking on the reproductive function and lipid metabolism of female rats.

Hershberger Assays for Bisphenol-A and Its Substitute Candidates.

Bisphenol-A(BPA) is a member of alkylphenol family, and shows adverse effects including reduced fertility, reproductive tract abnormalities, metabolic disorder, cancer induction, neurotoxicity and immunotoxicity. In the present study, we conducted Hershberger assay to evaluate whether the two candidates to replace BPA have androgenic or antiandrogenic activity. The assay was carried out using immature castrated Sprague-Dawley male rats. After 7 days of the surgery, testosterone propionate (TP, 0.4 mg/kg/day) and test materials (low dose, 40 mg/kg/day; high dose, 400 mg/kg/day) were administered for 10 consecutive days by subcutaneous (s.c.) injection and oral gavage, respectively. Test materials were BPA, isosorbide (ISO) and cyclohexanedimethanol (CHDM). The rats were necropsied, and then the weights of five androgen-dependent tissues [ventral prostate, seminal vesicle, levator ani-bulbocavernosus (LABC) muscle, paired Cowper's glands, and glans penis] and three androgen-insensitive tissues (kidney, spleen and liver) were measured. All test materials including BPA did not exhibit any androgenic activity in the assay. On the contrary, antiandrogen-like activities were found in all test groups, and the order of the intensity was CHDM > BPA > ISO in the five androgen-sensitive tissues. There was no statistical difference between low dose treatment and high dose treatment of BPA group as well as ISO group. In CHDM group, high dose treatment exhibited most severe weight reduction in all measured tissues. There was no statistical difference in androgen-insensitive tissue measurements, except BPA groups. Since the effects of ISO treatment on the accessory sex organs were much less or not present at all when compared to those of BPA, ISO could be a strong candidate to replace BPA. CHDM treatment brought most severe weight reduction in all of androgen-sensitive tissues, so this material should be excluded for further screening of BPA substitute selection.

Determination of self-exchange rate of alkanethiolates in self-assembled monolayers on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

In this paper, we describe a new method for determining the exchange rates of alkanethiolates in self-assembled monolayers (SAMs) on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the compositions of the alkanethiolate in SAMs rapidly and directly. In particular, to investigate the self-exchange of alkanethiols, we prepared a deuterated alkanethiol that has the same molecular properties as the non-deuterated alkanethiol but a different molecular weight. SAMs consisting of deuterated alkanethiolates were immersed in a solution of the non-deuterated alkanethiol, and the influences of the immersion time, temperature, concentration, and solvent on the self-exchange rates were investigated. Furthermore, we assessed the exchange rates among alkanethiols with different carbon chain lengths and different size of ethylene glycol units. In addition, we performed molecular dynamics simulations using a model SAM system in order to understand the molecular mechanism of the exchange process.

Free energy of PAMAM dendrimer adsorption onto model biological membranes.

We investigated the thermodynamic, structural, and dynamics changes in dendrimer-membrane systems during dendrimer adsorption to biological membrane systems by combining atomistic molecular dynamics simulations with umbrella sampling techniques to understand the atomistic interactions between the dendrimer and biological membranes. An ethylenediamine core polyamidoamine dendrimer (generation 3) with amine terminal groups and both zwitterionic dipalmitoyl-phosphatidyl-choline (DPPC) and anionic palmitoyl-oleoyl-phosphatidyl glycerol (POPG) lipid bilayer membranes were used as the model dendrimer and biological membranes, respectively, in this study. The free energy of the dendrimer adsorption onto two model membranes with different charge states was quantitatively determined. For the zwitterionic DPPC membrane, the dendrimer has a minimum free energy of approximately 50 kcal/mol, which is 15 kcal/mol higher than that observed in previous studies. The dominant contribution to the adsorption potential energy is the van der Waals attraction between the dendrimer and the DPPC membrane. However, the anionic POPG membrane pulls the positively charged dendrimer with an attractive mean force of about 200 pN, finally positioning the dendrimer in the membrane headgroup region. As a result of these strong attractive dendrimer and membrane interactions, the dendrimer structurally undergoes the transition from spherical to a pancake conformation, which slows its lateral mobility, especially in the presence of the POPG membrane. The bilayer lipid membranes are also perturbed by the dendrimer adsorption.

Neuroprotective effects of Eucommia ulmoides Oliv. Bark on amyloid beta(25-35)-induced learning and memory impairments in mice.

In the present study, we examined whether aqueous extract of Eucommia ulmoides Oliv. Bark (EUE) with graded doses exerted its neuroprotective effects on amyloid beta(25-35) (Aß(25-35))-induced learning and memory impairments in mice. Mice received a single intracerebroventricular (i.c.v.) injection of Aß(25-35) 6 nmol as the critical factor in Alzheimer's disease (AD), cognition was evaluated using Y-maze, passive avoidance, and Morris water maze tests. EUE significantly improved the Aß(25-35)-induced memory deficit in the Y-maze test. Also, EUE increased step-through latency time with Aß(25-35)-induced learning and memory deficits in the passive avoidance test. In addition, EUE decreased the escape latencies with Aß(25-35)-induced cognitive impairments in the Morris water maze test. In the probe trial session, EUE increased time spent in the target quadrant. In the in vitro study, EUE was found to inhibit acetylcholinesterase (AChE) activity in a dose-dependent manner (IC50 value; 172 µg/ml). Ex vivo study, EUE significantly inhibited AChE activity in the hippocampus and frontal cortex. These results demonstrate that EUE possesses potent neuroprotective effects and that its beneficial effects are mediated, in part, by AChE inhibition, and therefore, might be a potential candidate in neurodegenerative diseases such as AD.

Neuroprotective effects of chlorogenic acid on scopolamine-induced amnesia via anti-acetylcholinesterase and anti-oxidative activities in mice.

Chlorogenic acid is a major polyphenolic component of many plants and beverages, and is particularly abundant in coffee. We evaluated the neuroprotective effects of chlorogenic acid on learning and memory impairment induced by scopolamine (0.5 mg/kg, i.p.), a muscarinic antagonist, using the Y-maze, passive avoidance, and Morris water maze tests. The chlorogenic acid significantly improved the impairment of short-term or working memory induced by scopolamine in the Y-maze test, and significantly reversed cognitive impairments in mice as measured by the passive avoidance test. In addition, chlorogenic acid decreased escape latencies in the Morris water maze test. In a probe trial session, chlorogenic acid increased the latency time in the target quadrant in a dose-dependent manner. Ex vivo, chlorogenic acid inhibited acetylcholinesterase activity in the hippocampus and frontal cortex. Chlorogenic acid also decreased malondialdehyde levels in the hippocampus and frontal cortex. In vitro, chlorogenic acid was found to inhibit acetylcholinesterase activity (IC50=98.17 µg/ml) and free radical scavenging activity (IC50=3.09 µg/ml) in a dose-dependent manner. These results indicate that chlorogenic acid may exert anti-amnesic activity via inhibition of acetylcholinesterase and malondialdehyde in the hippocampus and frontal cortex.

ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.

ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration.

Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry.

The human proteome is a highly complex extension of the genome wherein a single gene often produces distinct protein forms due to alternative splicing, RNA editing, polymorphisms, and posttranslational modifications. Such biological variation compounded by the high sequence identity within gene families currently overwhelms the complete and routine characterization of mammalian proteins by MS. A new data base of human proteins (and their possible variants) was created and searched using tandem mass spectrometric data from intact proteins. This first application of top down MS/MS to wild-type human proteins demonstrates both gene-specific identification and the unambiguous characterization of multifaceted mass shifts (Deltam values). Such Deltam values found from the precise identification of 45 protein forms from HeLa cells reveal 34 coding single nucleotide polymorphisms, two protein forms from alternative splicing, and 12 diverse modifications (not including simple N-terminal processing), including a previously unknown phosphorylation at 10% occupancy. Automated protein identification was achieved with a median expectation value of 10(-13) and often occurred simultaneously with dissection of diverse sources of protein variability as they occur in combination. Top down MS therefore has a bright future for enabling precise annotation of gene products expressed from the human genome by non-mass spectrometrists.