Characterization and identification of dityrosine cross-linked peptides using tandem mass spectrometry

The use of mass spectrometry coupled with chemical cross-linking of proteins has become a powerful tool for proteins structure and interactions studies. Unlike structural analysis of proteins using chemical reagents specific for lysine or cysteine residues, identification of gas-phase fragmentation patterns of endogenous dityrosine cross-linked peptides have not been investigated. Dityrosine cross-linking in proteins and peptides are clinical markers of oxidative stress, aging, and neurodegenerative diseases including Alzheimer’s disease and Parkinson’s disease. In this study, we investigated and characterized the fragmentation pattern of a synthetically prepared dityrosine cross-linked dimer of Aβ(1–16) using ESI tandem mass spectrometry. We then detailed the fragmentation pattern of dityrosine cross-linked Aβ(1–16), using collision induced dissociation (CID), higher-energy collision induced dissociation (HCD), electron transfer dissociation (ETD), and electron capture dissociation (ECD). Application of these generic fragmentation rules of dityrosine cross-linked peptides allowed for the identification of dityrosine cross-links in peptides of Aβ and α-synuclein generated in vitro by enzymatic peroxidation. We report, for the first time, the dityrosine cross-linked residues in human hemoglobin and α-synuclein under oxidative conditions. Together these tools open up the potential for automated analysis of this naturally occurring post-translation modification in neurodegenerative diseases as well as other pathological conditions

Crystallization and preliminary crystallographic analysis of the signal recognition particle SRPΦ14-9 fusion protein

The SRPphi14-9 fusion protein, which can functionally replace the SRP9/14 heterodimer in the mammalian signal recognition particle (SRP), has been crystallized using the vapor diffusion method. Four different crystal forms were grown. SRPphi14-9 form IV crystals belong to the space group P4(1)22/ P4(3)22 with cell parameters a = b = 69.7 Angstroms, c = 95.7 Angstroms, alpha = beta = gamma = 90 degrees. A complete data set to 2.8 Angstroms resolution with an Rsym on intensities of 7.0% was collected on a single flash-frozen crystal

iPRG-2013 Proteome Informatics Research Group study: Using RNA-seq data to refine proteomic data analysis

The Proteome Informatics Research Group (iPRG) this year performed a study to evaluate the benefits of using databases derived from RNA-Seq data for peptide identification. The proteomic dataset provided consisted of high mass accuracy tandem mass spectra acquired when analyzing human peripheral blood mononuclear cells. A variety of different types of sequence databases were supplied. These included a standard protein sequence database; a database containing only sequences of proteins expressed in the sample based on RNA-Seq data; a database that included sequence and splice variants; a database of sequences that could not be reconciled to known expressed gene sequences. Participants were asked to report spectral identifications in the form of an Excel spreadsheet, highlighting those identifications that were only identified using one of the RNA-Seq derived specialized sequence databases. Participants were also required to complete a web-based questionnaire summarizing the tools and methods they used. Additional peptide identifications were achieved by the use of each of the different RNA-Seq derived databases, although the number of additional identifications was modest. Nevertheless, these new identifications could have potential biological significance, so this type of analysis may still be worthwhile

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments

Proteomic

Proteomics Standards Initiative Extended FASTA Format.

Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI extended FASTA format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backward compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available at http://www.psidev.info/peff

Análise descritiva quantitativa do palmito de pupunheira Quantitative descriptive analysis of pejibaye palm heart

Este estudo foi conduzido para descrever o perfil sensorial do palmito de pupunha. A análise descritiva quantitativa (ADQ) foi utilizada para descrever os atributos sensoriais relacionados à aparência, aroma, e textura de três marcas comerciais de palmito de pupunha. As amostras foram avaliadas por uma equipe selecionada com onze provadores e foram definidos nove atributos sensoriais: cor amarela, aparência uniforme e úmida, aroma e sabor não característicos, sabor acido, residual acido e textura macia. Houve diferenças significativas em seis atributos entre as três marcas testadas. Os provadores descreveram os palmitos de pupunha como: cor amarela clara, aparência uniforme e úmida, aroma e sabor não característicos e sabor ácido com valores intermediários, residual acido e amargor final com valores de pouco e textura muito macia a uma textura intermediária.<br>This research was carried out to establish the sensory profile of pejibaye palm heart. The quantitative descriptive analysis was used to establish the sensory attributes related to appearance, flavor, taste and texture of tree commercial marks of pejibaye palm heart. These samples were evaluated by eleven trained panelists who described nine sensory attributes: yellow color, uniform and humid appearance, non-characteristic aroma and flavor, acid flavor, residual acid taste, and soft texture. There were significant differences in six attributes among the three tested marks. Panelists described the pejibaye palm heart as: light yellow color, uniform and humid appearance, non-characteristic aroma and flavor, acid flavor with medium values, acid residual taste and bitterness final taste from little values and high soft texture to an medium value texture