Unknown Modifications Research Articles

Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications.

We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.

Sirtuins and Novel Protein Post Translational Modifications

Sirtuins are a class of enzymes known as nicotinamide adenine dinucleotide (NAD)‐dependent deacetylases. Sirtuins regulate aging, transcription, and metabolism, and are important targets for treating several human diseases. There are seven sirtuins in humans, SIRT1‐7. Four of them (SIRT4‐7) have very weak deacetylase activity, which have caused many confusions and debates in the biological community. My laboratory has recently discovered several novel enzymatic activities, such as desuccinylation and defatty‐acylation, for several sirtuins with no robust deacetylase activity. This have led to the identification of previously unknown protein posttranslational modifications and revealed new biological functions of sirtuins, such as the regulation of protein secretion.

Characterization of the E. coli proteome and its modifications during growth and ethanol stress.

We set out to provide a resource to the microbiology community especially with respect to systems biology based endeavors. To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in a systematic fashion during growth and ethanol stress in E. coli. We utilized high-resolution mass spectrometry (MS) combined with the Super-SILAC approach. In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ). The dynamic range of protein expression spanned up to six orders of magnitude, with the highest protein copy per cell estimated at approximately 300,000. We focused on the proteome dynamics involved during stationary phase growth. A global up-regulation of proteins related to stress response was detected in later stages of growth. We observed the down-regulation of the methyl directed mismatch repair system containing MutS and MutL of E. coli growing in long term growth cultures, confirming that higher incidence of mutations presents an important mechanism in the increase in genetic diversity and stationary phase survival in E. coli. During ethanol stress, known markers such as alcohol dehydrogenase and aldehyde dehydrogenase were induced, further validating the dataset. Finally, we performed unbiased protein modification detection and revealed changes of many known and unknown protein modifications in both experimental conditions. Data are available via ProteomeXchange with identifier PXD001648.

Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin (HSA)

This work presents a method for creating a mass spectral library containing tandem spectra of identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA(1)) was selected for this purpose owing to its ubiquity, high level of characterization and availability of digest data. The underlying experimental data consisted of ∼3000 one-dimensional LC-ESI-MS/MS runs with ion-trap fragmentation. In order to generate a wide range of peptides, studies covered a broad set of instrument and digestion conditions using multiple sources of HSA and trypsin. Computer methods were developed to enable the reliable identification and reference spectrum extraction of all peptide ions identifiable by current sequence search methods. This process made use of both MS2 (tandem) spectra and MS1 (electrospray) data. Identified spectra were generated for 2918 different peptide ions, using a variety of manually-validated filters to ensure spectrum quality and identification reliability. The resulting library was composed of 10% conventional tryptic and 29% semitryptic peptide ions, along with 42% tryptic peptide ions with known or unknown modifications, which included both analytical artifacts and post-translational modifications (PTMs) present in the original HSA. The remaining 19% contained unexpected missed-cleavages or were under/over alkylated. The methods described can be extended to create equivalent spectral libraries for any target protein. Such libraries have a number of applications in addition to their known advantages of speed and sensitivity, including the ready re-identification of known PTMs, rejection of artifact spectra and a means of assessing sample and digestion quality.

ISPTM: An Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in nuclear matrix associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification compared with that of the conventional all-in-one search approach, and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures.

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA

N6-methyladenosine (m6A) is a prevalent internal modification in mRNA and non- coding RNA affecting various cellular pathways. Here we report the discovery of two additional modifications, N6-hydroxymethyladenosine (hm6A) and N6- formyladenosine (f6A), in mammalian mRNA. We show that FeII- and α-ketoglutarate (α-KG)-dependent fat mass and obesity associated (FTO) protein oxidizes m6A to generates hm6A as an intermediate modification and f6A as a further oxidized product. hm6A and f6A have half-life times of ~3 h in aqueous solution under physiological relevant conditions, and are present in isolated mRNA from human cells as well as mouse tissues. These previously unknown modifications derived from the prevalent m6A in mRNA, formed through oxidative RNA demethylation, may dynamically modulate RNA-protein interactions to affect gene expression regulation.

Byonic: advanced peptide and protein identification software.

Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available, facilitates a much wider range of search possibilities than previous search software such as SEQUEST and Mascot. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Hence, Byonic can search for tens or even hundreds of modification types simultaneously without a prohibitively large combinatorial explosion. Byonic's Wildcard Search allows the user to search for unanticipated or even unknown modifications alongside known modifications. Finally, Byonic's Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites.

Characterization of Modified RNA by Top‐Down Mass Spectrometry

Characterization of Modified RNA by Top‐Down Mass Spectrometry

Comprehensive identification of novel post‐translational modifications in cellular peroxiredoxin 6

Peroxiredoxin 6 (PRDX6), a 1-Cys peroxiredoxin, is a bifunctional enzyme acting both as a glutathione peroxidase and a phospholipase A2. However, the underlying mechanisms and their regulation mechanisms are not well understood. Because post-translational modifications (PTMs) have been shown to play important roles in the function of many proteins, we undertook, in this study, to identify the PTMs in PRDX6 utilizing proteomic tools including nanoUPLC-ESI-q-TOF MS/MS employing selectively excluded mass screening analysis (SEMSA) in conjunction with MOD(i) and MODmap algorithm. We chose PRDX6 obtained from liver tissues from two inbred mouse strains, C57BL/6J and C3H/HeJ, which vary in their susceptibility to high-fat diet-induced obesity and atherosclerosis, and a B16F10 melanoma cell line for this study. When PRDX6 protein samples were separated on 2D-PAGE based on pI, several PRDX6 spots appeared. They were purified and the low abundant PTMs in each PRDX6 spot were analyzed. Unexpected mass shifts (Δm = -34, +25, +64, +87, +103, +134, +150, +284 Da) observed at active site cysteine residue (Cys47) were quantified using precursor ion intensities. Mass differences of -34, +25, and +64 Da are presumed to reflect the conversion of cysteine to dehydroalanine, cyano, and Cys-SO(2) -SH, respectively. We also detected acrylamide adducts of sulfenic and sulfinic acids (+87 and +103 Da) as well as unknown modifications (+134, +150, +284 Da). Comprehensive analysis of these PTMs revealed that the PRDX6 exists as a heterogeneous mixture of molecules containing a multitude of PTMs. Several of these modifications occur at cysteine residue in the enzyme active site. Other modifications observed, in PRDX6 from mouse liver tissues included, among others, mono- and dioxidation at Trp and Met, acetylation at Lys, and deamidation at Asn and Gln. Comprehensive identification of the diverse PTMs occurring in this bifunctional PRDX6 enzyme should help understand how PRDX6 plays key roles in oxidative stresses.

Molecular phylogenetics by direct comparison of tandem mass spectra

Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications.

Chemical modificomics: a novel strategy for efficient biomarker discovery through chemical modifications on a target peptide

This manuscript describes a proof-of-concept study to develop a novel “omics” strategy, referred to as “chemical modificomics”, for efficient biomarker discovery. Proteins and peptides are exposed to higher chemical stresses during some physiological events, such as increased oxidative stress from the degenerative diseases of aging. Therefore, the resulting chemical modifications can provide significant information about biological events. However, quantitative analyses of bioactive peptides and proteins in specific diseases have relied almost exclusively on the use of immunoassay-based procedures, without concern for possible chemical modifications and subsequent changes of activity/conformation. Therefore, we focused only on specific bioactive peptides and proteins closely related to a target disease, and exhaustively screened all chemical modifications for efficient biomarker discovery. The strategy involves two tactics: (1) backbone-specific clean-up methodology by recycling commercially available antibodies and (2) mass spectrometric screening methodology to provide an overview of unknown chemical modifications on a specific target. In this study, seven chemically modified angiotensin (Ang) IIs were employed as model compounds. The clean-up was conducted by immunoaffinity purification using commercially available anti-Ang II antibody (polyclonal). Screening was then performed by precursor ion scan using y2 ion, which is a common C-terminal fragment without including the modifications. This strategy can be simply applied to screen various chemical modifications including posttranslational modifications on a specific peptide and protein analyzed by immunological methods.

Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data

Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.

Experimental study of the substructure isolation method for local health monitoring

SUMMARY This paper extends and studies experimentally the substructure isolation method. Local health monitoring is significant for large and complex structures, since it costs less and can be easily implemented compared with global analysis. In contrast to other substructuring methods, in which the substructure is separated from the global structure, but coupled to it via the interface forces, the substructure isolation method isolates the substructure into an independent structure by placing virtual fixed supports on the interface. Model updating or damage identification can be then performed locally and precisely using the constructed responses of the isolated substructure and any of the existing methods aimed originally at global identification. This paper discusses and further extends the approach to improve its performance in real applications. A new type of virtual interface support (free support) is proposed for isolation. Relaxation of the original requirements concerning the type and placement of the isolating excitations is discussed. Previously, the method relied on the linearity of the global structure; here, only the substructure is required to be linear, the global structure besides the substructure can be non-linear, yielding, changing or unknown. A damaged cantilever beam is used in the experimental study. Up to three modified global structures with the same substructure are used to test the robustness of the isolation with respect to unknown modifications and non-linearities of the outside structure. Two typical global health monitoring methods are applied at the substructural level. A comparison with the results obtained from a generic substructure separation method is offered. Copyright © 2011 John Wiley & Sons, Ltd.

Diversity of cyanobacteria in man-made solar saltern, Petchaburi Province, Thailand - a pilot study.

Solar salterns can be found in many tropical and subtropical regions throughout the world, however, nothing is known from these habitats in Southeast Asia. The Petchaburi solar salterns are located in Petchaburi Province, middle part of Thailand. These areas can be defined as hypersaline biotopes where, in salt-producing times, salinity increases by more than 10 times that of seawater. The annual salinity gradient of these areas ranges from 0 - 35 ppt. in the non salt-producing period and gradually elevates from more than 35 ppt. up to saturation in the salt producing period, when salt crystals are formed. The cyanobacterial samples were collected from four ponds of the Petchaburi saltern during the salt producing period (November - December 2009), when the range of salinity was from 90 - 250 ppt. pH values of soil samples ranged from 7.9 - 8.1 and conductivity from 164 - 350 dS/m. Other physico-chemical parameters were analyzed in the soil samples as well. Cyanobacterial mats and their filaments predominated among the diatoms. Sixteen species of cyanobacteria were found. Dominant species were Spirulina subsalsa, Coleofasciculus cf. chthonoplastes and Oscillatoria lloydiana. Most of the species found in this study have not yet been reported in Thailand. Species, which did not correspond to any described taxa in scientific literature (new species or unknown modifications) are designated by "cf." or "sp.".

Profiling Cys34 Adducts of Human Serum Albumin by Fixed-Step Selected Reaction Monitoring

A method is described for profiling putative adducts (or other unknown covalent modifications) at the Cys34 locus of human serum albumin (HSA), which represents the preferred reaction site for small electrophilic species in human serum. By comparing profiles of putative HSA-Cys34 adducts across populations of interest it is theoretically possible to explore environmental causes of degenerative diseases and cancer caused by both exogenous and endogenous chemicals. We report a novel application of selected-reaction-monitoring (SRM) mass spectrometry, termed fixed-step SRM (FS-SRM), that allows detection of essentially all HSA-Cys34 modifications over a specified range of mass increases (added masses). After tryptic digestion, HSA-Cys34 adducts are contained in the third largest peptide (T3), which contains 21 amino acids and an average mass of 2433.87 Da. The FS-SRM method does not require that exact masses of T3 adducts be known in advance but rather uses a theoretical list of T3-adduct m/z values separated by a fixed increment of 1.5. In terms of added masses, each triply charged parent ion represents a bin of ±2.3 Da between 9.1 Da and 351.1 Da. Synthetic T3 adducts were used to optimize FS-SRM and to establish screening rules based upon selected b- and y-series fragment ions. An isotopically labeled T3 adduct is added to protein digests to facilitate quantification of putative adducts. We used FS-SRM to generate putative adduct profiles from six archived specimens of HSA that had been pooled by gender, race, and smoking status. An average of 66 putative adduct hits (out of a possible 77) were detected in these samples. Putative adducts covered a wide range of concentrations, were most abundant in the mass range below 100 Da, and were more abundant in smokers than in nonsmokers. With minor modifications, the FS-SRM methodology can be applied to other nucleophilic sites and proteins.

Novel Oxidative Modifications in Redox-Active Cysteine Residues

Redox-active cysteine, a highly reactive sulfhydryl, is one of the major targets of ROS. Formation of disulfide bonds and other oxidative derivatives of cysteine including sulfenic, sulfinic, and sulfonic acids, regulates the biological function of various proteins. We identified novel low-abundant cysteine modifications in cellular GAPDH purified on 2-dimensional gel electrophoresis (2D-PAGE) by employing selectively excluded mass screening analysis for nano ultraperformance liquid chromatography-electrospray-quadrupole-time of flight tandem mass spectrometry, in conjunction with MODi and MODmap algorithm. We observed unexpected mass shifts (Δm=-16, -34, +64, +87, and +103 Da) at redox-active cysteine residue in cellular GAPDH purified on 2D-PAGE, in oxidized NDP kinase A, peroxiredoxin 6, and in various mitochondrial proteins. Mass differences of -16, -34, and +64 Da are presumed to reflect the conversion of cysteine to serine, dehydroalanine (DHA), and Cys-SO2-SH respectively. To determine the plausible pathways to the formation of these products, we prepared model compounds and examined the hydrolysis and hydration of thiosulfonate (Cys-S-SO2-Cys) either to DHA (Δm=-34 Da) or serine along with Cys-SO2-SH (Δm=+64 Da). We also detected acrylamide adducts of sulfenic and sulfinic acids (+87 and +103 Da). These findings suggest that oxidations take place at redox-active cysteine residues in cellular proteins, with the formation of thiosulfonate, Cys-SO2-SH, and DHA, and conversion of cysteine to serine, in addition to sulfenic, sulfinic and sulfonic acids of reactive cysteine.

Rex1/Zfp42 as an epigenetic regulator for genomic imprinting

Zfp42/Rex1 (reduced expression gene 1) is a well-known stem-cell marker that has been duplicated from YY1 in the eutherian lineage. In the current study, we characterized the in vivo roles of Rex1 using a mutant mouse line disrupting its transcription. In contrast to the ubiquitous expression of YY1, Rex1 is expressed only during spermatogenesis and early embryogenesis and also in a very limited area of the placenta. Yet, the gene dosage of Rex1 is very critical for the survival of the late-stage embryos and neonates. This delayed phenotypic consequence suggests potential roles for Rex1 in establishing and maintaining unknown epigenetic modifications. Consistently, Rex1-null blastocysts display hypermethylation in the differentially methylated regions (DMRs) of Peg3 and Gnas imprinted domains, which are known to contain YY1 binding sites. Further analyses confirmed in vivo binding of Rex1 only to the unmethylated allele of these two regions. Thus, Rex1 may function as a protector for these DMRs against DNA methylation. Overall, the functional connection of Rex1 to genomic imprinting represents another case where newly made genes have co-evolved with lineage-specific phenomena.

Novel missense mutations in exon 15 of desmoglein-2: Role of the intracellular cadherin segment in arrhythmogenic right ventricular cardiomyopathy?

BackgroundThe diagnosis of arrhythmogenic right ventricular cardiomyopathy can be challenging. Disease-causing mutations in desmosomal genes have been identified. A novel diagnostic feature, loss of immunoreactivity for plakoglobin from the intercalated disks, recently was proposed.ObjectiveThe purpose of this study was to identify two novel mutations in the intracellular cadherin segment of desmoglein-2 (G812S and C813R in exon 15). Co-segregation of the G812S mutation with disease expression was established in a large Caucasian family. Endomyocardial biopsies of two individuals showed reduced plakoglobin signal at the intercalated disk.MethodsTo understand the pathologic changes occurring in the diseased myocardium, functional studies on three mutations in exon 15 of desmoglein-2 (G812C, G812S, C813R) were performed.ResultsLocalization studies failed to detect any differences in targeting or stability of the mutant proteins, suggesting that they act via a dominant negative mechanism. Binding assays were performed to probe for altered binding affinities toward other desmosomal proteins, such as plakoglobin and plakophilin-2. Although no differences were observed for the mutated proteins in comparison to wild-type desmoglein-2, binding to plakophilin-2 depended on the expression system (i.e., bacterial vs mammalian protein expression). In addition, abnormal migration of the C813R mutant protein was observed in gel electrophoresis.ConclusionLoss of plakoglobin immunoreactivity from the intercalated disks appears to be the endpoint of complex pathologic changes, and our functional data suggest that yet unknown posttranslational modifications of desmoglein-2 might be involved.

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction.

BackgroundWhen generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown.ResultsWe show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya).ConclusionWe believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

Large-Scale Identification and Quantification of Covalent Modifications in Therapeutic Proteins

Covalent modifications on therapeutic proteins are traditionally monitored by chromatographic techniques, which quantify limited number of protein modifications at a time. In this report, computer algorithms for automated analyses of liquid chromatography/tandem mass spectrometry (LC/MS/MS) data for large-scale identification and quantification of known and unknown modifications are described. Peptide identification is achieved by comparing the experimental fragmentation spectrum to the predicted spectrum of each native or modified peptide. Peak areas of related peptide ions under their selected-ion chromatograms (SIC) are used for relative quantification of modified peptides. A matched window function is used to generate SIC for more reliable quantification. In an LC/MS/MS analysis of a tryptic digestion of an IgG2 monoclonal antibody, 1712 peptide ions were identified with a false-discovery rate of approximately 0.4%, and 227 modifications were identified and quantified. The accuracy of the mass spectrometry-based quantification is evaluated by comparing the abundance of different glycoforms determined by mass spectrometry to that determined by a fluorescence-based chromatography method. This large-scale method may potentially replace many chromatographic methods for assessing the quality attributes of therapeutic proteins.