A Ratiometric Catalog of Protein Isoform Shifts in the Cardiac Fetal Gene Program.

The fetal genetic program orchestrates cardiac development and the re-expression of fetal genes is thought to underlie cardiac disease and adaptation. Here, a proteomics ratio test using mass spectrometry is applied to find protein isoforms with statistically significant usage differences in the fetal vs. postnatal mouse heart. Changes in isoform usage ratios are pervasive at the protein level, with 104 significant events observed, including 88 paralog-derived isoform switching events and 16 splicing-derived isoform switching events between fetal and postnatal hearts. The ratiometric proteomic comparisons rediscovered hallmark fetal gene signatures including a postnatal switch from fetal ß (MYH7) toward ɑ (MYH6) myosin heavy chains and from slow skeletal muscle (TNNI1) toward cardiac (TNNI3) troponin I. Altered usages in metabolic proteins are prominent, including a platelet to muscle phosphofructokinase (PFKP - PFKM), enolase 1 to 3 (ENO1 - ENO3), and alternative splicing of pyruvate kinase M2 toward M1 (PKM2 - PKM1) isoforms in glycolysis. The data also revealed a parallel change in mitochondrial proteins in cardiac development, suggesting the shift toward aerobic respiration involves also a remodeling of the mitochondrial protein isoform proportion. Finally, a number of glycolytic protein isoforms revert toward their fetal forms in adult hearts under pathological cardiac hypertrophy, suggesting their functional roles in adaptive or maladaptive response, but this reversal is partial. In summary, this work presents a catalog of ratiometric protein markers of the fetal genetic program of the mouse heart, including previously unreported splice isoform markers.

Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.

A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched with intrinsically disordered regions. Moreover, over two-thirds of such regions are predicted to function in protein binding and RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.

Protocol for the prediction, interpretation, and mutation evaluation of post-translational modification using MIND-S.

Post-translational modifications (PTMs) serve as key regulatory mechanisms in various cellular processes; altered PTMs can potentially lead to human diseases. We present a protocol for using MIND-S (multi-label interpretable deep-learning approach for PTM prediction-structure version), to study PTMs. This protocol consists of step-by-step guide and includes three key applications of MIND-S: PTM predictions based on protein sequences, important amino acids identification, and elucidation of altered PTM landscape resulting from molecular mutations. For complete details on the use and execution of this protocol, please refer to Yan et al (2023).1.

Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.

A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched in intrinsically disordered regions, and over two-thirds of such regions are predicted to function in protein binding and/or RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.

MIND-S is a deep-learning prediction model for elucidating protein post-translational modifications in human diseases.

We present a deep-learning-based platform, MIND-S, for protein post-translational modification (PTM) predictions. MIND-S employs a multi-head attention and graph neural network and assembles a 15-fold ensemble model in a multi-label strategy to enable simultaneous prediction of multiple PTMs with high performance and computation efficiency. MIND-S also features an interpretation module, which provides the relevance of each amino acid for making the predictions and is validated with known motifs. The interpretation module also captures PTM patterns without any supervision. Furthermore, MIND-S enables examination of mutation effects on PTMs. We document a workflow, its applications to 26 types of PTMs of two datasets consisting of ∼50,000 proteins, and an example of MIND-S identifying a PTM-interrupting SNP with validation from biological data. We also include use case analyses of targeted proteins. Taken together, we have demonstrated that MIND-S is accurate, interpretable, and efficient to elucidate PTM-relevant biological processes in health and diseases.

Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy.

Cysteine oxidative modification of cellular proteins is crucial for many aspects of cardiac hypertrophy development. However, integrated dissection of multiple types of cysteine oxidative post-translational modifications (O-PTM) of proteomes in cardiac hypertrophy is currently missing. Here we developed a novel discovery platform that encompasses a customized biotin switch-based quantitative proteomics pipeline and an advanced analytic workflow to comprehensively profile the landscape of cysteine O-PTM in an ISO-induced cardiac hypertrophy mouse model. Specifically, we identified a total of 1655 proteins containing 3324 oxidized cysteine sites by at least one of the following three modifications: reversible cysteine O-PTM, cysteine sulfinylation (CysSO2H), and cysteine sulfonylation (CysSO3H). Analyzing the hypertrophy signatures that are reproducibly discovered from this computational workflow unveiled four biological processes with increased cysteine O-PTM. Among them, protein phosphorylation, creatine metabolism, and response to elevated Ca2+ pathways exhibited an elevation of cysteine O-PTM in early stages, whereas glucose metabolism enzymes were increasingly modified in later stages, illustrating a temporal regulatory map in cardiac hypertrophy. Our cysteine O-PTM platform depicts a dynamic and integrated landscape of the cysteine oxidative proteome, through the extracted molecular signatures, and provides critical mechanistic insights in cardiac hypertrophy. Data are available via ProteomeXchange with identifier PXD010336.

Quantitative temporal analysis of protein dynamics in cardiac remodeling.

Cardiac remodeling (CR) is a complex dynamic process common to many heart diseases. CR is characterized as a temporal progression of global adaptive and maladaptive perturbations. The complex nature of this process clouds a comprehensive understanding of CR, but greater insight into the processes and mechanisms has potential to identify new therapeutic targets. To provide a deeper understanding of this important cardiac process, we applied a new proteomic technique, PALM (Pulse Azidohomoalanine in Mammals), to quantitate the newly-synthesized protein (NSP) changes during the progression of isoproterenol (ISO)-induced CR in the mouse left ventricle. This analysis revealed a complex combination of adaptive and maladaptive alterations at acute and prolonged time points including the identification of proteins not previously associated with CR. We also combined the PALM dataset with our published protein turnover rate dataset to identify putative biochemical mechanisms underlying CR. The novel integration of analyzing NSPs together with their protein turnover rates demonstrated that alterations in specific biological pathways (e.g., inflammation and oxidative stress) are produced by differential regulation of protein synthesis and degradation.

Integrated omics dissection of proteome dynamics during cardiac remodeling.

Transcript abundance and protein abundance show modest correlation in many biological models, but how this impacts disease signature discovery in omics experiments is rarely explored. Here we report an integrated omics approach, incorporating measurements of transcript abundance, protein abundance, and protein turnover to map the landscape of proteome remodeling in a mouse model of pathological cardiac hypertrophy. Analyzing the hypertrophy signatures that are reproducibly discovered from each omics data type across six genetic strains of mice, we find that the integration of transcript abundance, protein abundance, and protein turnover data leads to 75% gain in discovered disease gene candidates. Moreover, the inclusion of protein turnover measurements allows discovery of post-transcriptional regulations across diverse pathways, and implicates distinct disease proteins not found in steady-state transcript and protein abundance data. Our results suggest that multi-omics investigations of proteome dynamics provide important insights into disease pathogenesis in vivo.

Cardiovascular proteomics in the era of big data: experimental and computational advances.

Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond merely inventorying protein species, and address sophisticated questions on cardiac physiology. The advent of massive mass spectrometry datasets has in turn led to increasing intersection between proteomics and big data science. Here we review new frontiers in technological developments and their applications to cardiovascular medicine. The impact of big data science on cardiovascular proteomics investigations and translation to medicine is highlighted.

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.

Amidst the proteomes of human tissues lie subsets of proteins that are closely involved in conserved pathophysiological processes. Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. With advances in proteomics technologies, it is now feasible to develop targeted proteomics assays that can accurately quantify protein abundance as well as their post-translational modifications; however, with rapidly accumulating number of studies implicating proteins in diseases, current resources are insufficient to target every protein without judiciously prioritizing the proteins with high significance and impact for assay development. We describe here a data science method to prioritize and expedite assay development on high-impact proteins across research fields by leveraging the biomedical literature record to rank and normalize proteins that are popularly and preferentially published by biomedical researchers. We demonstrate this method by finding priority proteins across six major physiological systems (cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal). The described method is data-driven and builds upon the collective knowledge of previous publications referenced on PubMed to lend objectivity to target selection. The method and resulting popular protein lists may also be useful for exploring biological processes associated with various physiological systems and research topics, in addition to benefiting ongoing efforts to facilitate the broad translation of proteomics technologies.

A large dataset of protein dynamics in the mammalian heart proteome.

Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.

Characterization of human plasma proteome dynamics using deuterium oxide.

PURPOSE: High-throughput quantification of human protein turnover via in vivo administration of deuterium oxide ((2) H2 O) is a powerful new approach to examine potential disease mechanisms. Its immediate clinical translation is contingent upon characterizations of the safety and hemodynamic effects of in vivo administration of (2) H2 O to human subjects. EXPERIMENTAL DESIGN: We recruited ten healthy human subjects with a broad demographic variety to evaluate the safety, feasibility, efficacy, and reproducibility of (2) H2 O intake for studying protein dynamics. We designed a protocol where each subject orally consumed weight-adjusted doses of 70% (2) H2 O daily for 14 days to enrich body water and proteins with deuterium. Plasma proteome dynamics was measured using a high-resolution MS method we recently developed. RESULTS: This protocol was successfully applied in ten human subjects to characterize the endogenous turnover rates of 542 human plasma proteins, the largest such human dataset to-date. Throughout the study, we did not detect physiological effects or signs of discomfort from (2) H2 O consumption. CONCLUSIONS AND CLINICAL RELEVANCE: Our investigation supports the utility of a (2) H2 O intake protocol that is safe, accessible, and effective for clinical investigations of large-scale human protein turnover dynamics. This workflow shows promising clinical translational value for examining plasma protein dynamics in human diseases.

Protein kinetic signatures of the remodeling heart following isoproterenol stimulation.

Protein temporal dynamics play a critical role in time-dimensional pathophysiological processes, including the gradual cardiac remodeling that occurs in early-stage heart failure. Methods for quantitative assessments of protein kinetics are lacking, and despite knowledge gained from single-protein studies, integrative views of the coordinated behavior of multiple proteins in cardiac remodeling are scarce. Here, we developed a workflow that integrates deuterium oxide (2H2O) labeling, high-resolution mass spectrometry (MS), and custom computational methods to systematically interrogate in vivo protein turnover. Using this workflow, we characterized the in vivo turnover kinetics of 2,964 proteins in a mouse model of ß-adrenergic-induced cardiac remodeling. The data provided a quantitative and longitudinal view of cardiac remodeling at the molecular level, revealing widespread kinetic regulations in calcium signaling, metabolism, proteostasis, and mitochondrial dynamics. We translated the workflow to human studies, creating a reference dataset of 496 plasma protein turnover rates from 4 healthy adults. The approach is applicable to short, minimal label enrichment and can be performed on as little as a single biopsy, thereby overcoming critical obstacles to clinical investigations. The protein turnover quantitation experiments and computational workflow described here should be widely applicable to large-scale biomolecular investigations of human disease mechanisms with a temporal perspective.

Laser-induced dissociation of singly protonated peptides at 193 and 266 nm within a hybrid linear ion trap mass spectrometer.

RATIONALE: We implemented, for the first time, laser-induced dissociation (LID) within a modified hybrid linear ion trap mass spectrometer, QTrap, while preserving the original scanning capabilities and routine performance of the instrument. METHODS: Precursor ions of interest were mass-selected in the first quadrupole (Q1), trapped in the radiofrequency-only quadrupole (q2), photodissociated under irradiation with a 193- or 266-nm laser beam in the third quadrupole (q3), and mass-analyzed using the linear ion trap. RESULTS: LID of singly charged protonated peptides revealed, in addition to conventional amide-bond cleavages, preferential fragmentation at Cα -C/N-Cα bonds of the backbone as well as at the Cα -Cß /Cß -Cγ bonds of the side-chains. The LID spectra of [M+H](+) featured product ions that were very similar to the observed radical-induced fragmentations in the CID spectra of analogous odd-electron radical cations generated through dissociative electron-transfer in metal-ligand-peptide complexes or through laser photolysis of iodopeptides. CONCLUSIONS: LID of [M+H](+) ions results in fragmentation channels that are comparable with those observed upon the CID of M(•+) ions, with a range of fascinating radical-induced fragmentations.

Arginine-facilitated isomerization: radical-induced dissociation of aliphatic radical cationic glycylarginyl(iso)leucine tripeptides.

The gas phase fragmentations of aliphatic radical cationic glycylglycyl(iso)leucine tripeptides ([G(•)G(L/I)](+)), with well-defined initial locations of the radical centers at their N-terminal α-carbon atoms, are significantly different from those of their basic glycylarginyl(iso)leucine ([G(•)R(L/I)](+)) counterparts; the former lead predominantly to [b(2) - H](•+) fragment ions, whereas the latter result in the formation of characteristic product ions via the losses of (•)CH(CH(3))(2) from [G(•)RL](+) and (•)CH(2)CH(3) from [G(•)RI](+) through C(ß)-C(γ) side-chain cleavages of the (iso)leucine residues, making these two peptides distinguishable. The α-carbon-centered radical at the leucine residue is the key intermediate that triggers the subsequent C(ß)-C(γ) bond cleavage, as supported by the absence of (•)CH(CH(3))(2) loss from the collision-induced dissociation of [G(•)RL(α-Me)](+), a radical cation for which the α-hydrogen atom of the leucine residue had been substituted by a methyl group. Density functional theory calculations at the B3LYP 6-31++G(d,p) level of theory supported the notion that the highly basic arginine residue could not only increase the energy barriers against charge-induced dissociation pathways but also decrease the energy barriers against hydrogen atom transfers in the GR(L/I) radical cations by ∼10 kcal mol(-1), thereby allowing the intermediate precursors containing α- and γ-carbon-centered radicals at the (iso)leucine residues to be formed more readily prior to promoting subsequent C(ß)-C(γ) and C(α)-C(ß) bond cleavages. The hydrogen atom transfer barriers for the α- and γ-carbon-centered GR(L/I) radical cations (roughly in the range 29-34 kcal mol(-1)) are comparable with those of the competitive side-chain cleavage processes. The transition structures for the elimination of (•)CH(CH(3))(2) and (•)CH(2)CH(3) from the (iso)leucine side chains possess similar structures, but slightly different dissociation barriers of 31.9 and 34.0 kcal mol(-1), respectively; the energy barriers for the elimination of the alkenes CH(2)═CH(CH(3))(2) and CH(3)CH═CHCH(3) through C(α)-C(ß) bond cleavages of γ-carbon-centered radicals at the (iso)leucine side chains are 29.1 and 32.8 kcal mol(-1), respectively.

Online combination of reversed-phase/reversed-phase and porous graphitic carbon liquid chromatography for multicomponent separation of proteomics and glycoproteomics samples.

In this paper, we describe an online combination of reversed-phase/reversed-phase (RP-RP) and porous graphitic carbon (PGC) liquid chromatography (LC) for multicomponent analysis of proteomics and glycoproteomics samples. The online RP-RP portion of this system provides comprehensive 2-D peptide separation based on sequence hydrophobicity at pH 2 and 10. Hydrophilic components (e.g. glycans, glycopeptides) that are not retained by RP are automatically diverted downstream to a PGC column for further trapping and separation. Furthermore, the RP-RP/PGC system can provide simultaneous extension of the hydropathy range and peak capacity for analysis. Using an 11-protein mixture, we found that the system could efficiently separate native peptides and released N-glycans from a single sample. We evaluated the applicability of the system to the analysis of complex biological samples using 25 µg of the lysate of a human choriocarcinoma cell line (BeWo), confidently identifying a total of 1449 proteins from a single experiment and up to 1909 distinct proteins from technical triplicates. The PGC fraction increased the sequence coverage through the inclusion of additional hydrophilic sequences that accounted for up to 6.9% of the total identified peptides from the BeWo lysate, with apparent preference for the detection of hydrophilic motifs and proteins. In addition, RP-RP/PGC is applicable to the analysis of complex glycomics samples, as demonstrated by our analysis of a concanavalin A-extracted glycoproteome from human serum; in total, 134 potentially N-glycosylated serum proteins, 151 possible N-glycosylation sites, and more than 40 possible N-glycan structures recognized by concanavalin A were simultaneously detected.

Arginine-facilitated α- and π-radical migrations in glycylarginyltryptophan radical cations.

We have used model tripeptides GXW (with X being one of the amino acid residues glycine (G), alanine (A), leucine (L), phenylalanine (F), glutamic acid (E), histidine (H), lysine (K), or arginine (R)) to study the effects of the basicity of the amino acid residue on the radical migrations and dissociations of odd-electron molecular peptide radical cations M(·+) in the gas phase. Low-energy collision-induced dissociation (CID) experiments revealed that the interconvertibility of the isomers [G(·)XW](+) (radical centered on the N-terminal α-carbon atom) and [GXW](·+) (radical centered on the π system of the indolyl ring) generally increased upon increasing the proton affinity of residue X. When X was arginine, the most basic amino acid, the two isomers were fully interconvertible and produced almost identical CID spectra despite the different locations of their initial radical sites. The presence of the very basic arginine residue allowed radical migrations to proceed readily among the [G(·)RW](+) and [GRW](·+) isomers prior to their dissociations. Density functional theory calculations revealed that the energy barriers for isomerizations among the α-carbon-centered radical [G(·)RW](+), the π-centered radical [GRW](·+), and the ß-carbon-centered radical [GRW(ß)(·)](+) (ca. 32-36 kcal mol(-1)) were comparable with those for their dissociations (ca. 32-34 kcal mol(-1)). The arginine residue in these GRW radical cations tightly sequesters the proton, thereby resulting in minimal changes in the chemical environment during the radical migrations, in contrast to the situation for the analogous GGW system, in which the proton is inefficiently stabilized during the course of radical migration.

Formation, isomerization, and dissociation of alpha-carbon-centered and pi-centered glycylglycyltryptophan radical cations.

Gas phase fragmentations of two isomeric radical cationic tripeptides of glycylglycyltryptophan-[G(*)GW](+) and [GGW](*+)-with well-defined initial radical sites at the alpha-carbon atom and the 3-methylindole ring, respectively, have been studied using collision-induced dissociation (CID), density functional theory (DFT), and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Substantially different low-energy CID spectra were obtained for these two isomeric GGW structures, suggesting that they did not interconvert on the time scale of these experiments. DFT and RRKM calculations were used to investigate the influence of the kinetics, stabilities, and locations of the radicals on the competition between the isomerization and dissociation channels. The calculated isomerization barrier between the GGW radical cations (>35.4 kcal/mol) was slightly higher than the barrier for competitive dissociation of these species (<30.5 kcal/mol); the corresponding microcanonical rate constants for isomerization obtained from RRKM calculations were all considerably lower than the dissociation rates at all internal energies. Thus, interconversion between the GGW isomers examined in this study cannot compete with their fragmentations.

Experimental and computational studies of the macrocyclic effect of an auxiliary ligand on electron and proton transfers within ternary copper(II)-histidine complexes.

The dissociation of [Cu(II)(L)His](*2+) complexes [L = diethylenetriamine (dien) or 1,4,7-triazacyclononane (9-aneN(3))] bears a strong resemblance to the previously reported behavior of [Cu(II)(L)GGH](*2+) complexes. We have used low-energy collision-induced dissociation experiments and density functional theory (DFT) calculations at the B3LYP/6-31+G(d) level to study the macrocyclic effect of the auxiliary ligands on the formation of His(*+) from prototypical [Cu(II)(L)His](*2+) systems. DFT revealed that the relative energy barriers of the same electron-transfer (ET) dissociation pathways of [Cu(II)(9-aneN(3))His](*2+) and [Cu(II)(dien)His](*2+) are very similar, with the ET reactions of [Cu(II)(9-aneN(3))His](*2+) leading to the generation of two distinct His(*+) species; in contrast, the proton transfer (PT) dissociation pathways of [Cu(II)(9-aneN(3))His](*2+) and [Cu(II)(dien)His](*2+) differ considerably. The PT reactions of [Cu(II)(9-aneN(3))His](*2+) are associated with substantially higher barriers (>13 kcal/mol) than those of [Cu(II)(dien)His](*2+). Thus, the sterically encumbered auxiliary 9-aneN(3) ligand facilitates ET reactions while moderating PT reactions, allowing the formation of hitherto nonobservable histidine radical cations.

Detection, characterization, and quantification of resveratrol glycosides in transgenic arabidopsis over-expressing a sorghum stilbene synthase gene by liquid chromatography/tandem mass spectrometry.

Transgenic Arabidopsis plants were analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS) to investigate the glycosylation patterns of resveratrol derived from expression of a sorghum stilbene synthase gene. In negative ionization mode, the different resveratrol derivatives fragmented to yield the diagnostic deprotonated resveratrol ion at m/z 227.2. The use of precursor ion scanning led to the identification of precursor ions for different resveratrol glycosides through rapid differentiation from other phytochemical constituents. Structural information was generated simultaneously from the low-collision-energy product ion spectra using hybrid linear ion-trap mass spectrometry. Three additional resveratrol-related metabolites - a resveratrol diglucoside (M1) and trans- and cis-resveratrol acetylhexosides (M2 and M3) - were detected in the crude plant extracts. The identities of M1, M2, and M3 were confirmed by accurate mass analysis on a quadrupole time-of-flight mass spectrometer as well as beta-glucosidase digestion or UV-induced isomerization. Quantitative analyses by LC/MS in multiple reaction monitoring mode revealed that resveratrol diglucoside and cis-resveratrol acetyhexoside accumulated up to 2.79 and 10.38 microg/g, respectively, while trans-resveratrol acetylhexoside was barely detectable. This study demonstrated the power of the hybrid linear ion-trap technology for simultaneous profiling and structural characterization of stilbene-related metabolites, which would be useful to understand how resveratrol is modified in sorghum and other plants.