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proteomics analysis tools

Bryan A Stanfill, Ernesto S Nakayasu, Lisa M Bramer, Allison M Thompson, Charles K Ansong, Therese Clauss, Marina A Gritsenko, Matthew E Monroe, Ronald J Moore, Daniel J Orton, Paul D Piehowski, Athena A Schepmoes, Richard D Smith, Bobbie-Jo Webb-Robertson, Thomas O Metz, The Environmental Determinants Of Diabetes In The Young Teddy Study Group
Liquid chromatography-mass spectrometry (LC-MS)-based proteomics studies of large sample cohorts can easily require from months to years to complete. Acquiring consistent, high-quality data in such large-scale studies is challenging because of normal variations in instrumentation performance over time, as well as artifacts introduced by the samples themselves, such as those due to collection, storage and processing. Existing quality control methods for proteomics data primarily focus on post-hoc analysis to remove low-quality data that would degrade downstream statistics; they are not designed to evaluate the data in near real-time, which would allow for interventions as soon as deviations in data quality are detected...
April 17, 2018: Molecular & Cellular Proteomics: MCP
Elizaveta M Solovyeva, Anna A Lobas, Arthur T Kopylov, Irina Y Ilina, Lev I Levitsky, Sergei A Moshkovskii, Mikhail V Gorshkov
Recent advances in mass spectrometry and separation technologies created the opportunities for deep proteome characterization using shotgun proteomics approaches. The "real world" sample complexity and high concentration range limit the sensitivity of this characterization. The common strategy for increasing the sensitivity is sample fractionation prior to analysis either at the protein or the peptide level. Typically, fractionation at the peptide level is performed using linear gradient high-performance liquid chromatography followed by uniform fraction collection...
April 17, 2018: Analytical and Bioanalytical Chemistry
Lin Chen, Wei Su, Hua Chen, Dan-Qian Chen, Ming Wang, Yan Guo, Ying-Yong Zhao
Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein...
2018: Advances in Clinical Chemistry
Immacolata Iovinella, Alison McAfee, Guido Mastrobuoni, Stefan Kempa, Leonard J Foster, Paolo Pelosi, Francesca Romana Dani
We have performed a proteomic analysis on chemosensory organs of Varroa destructor, the honey bee mite, in order to identify putative soluble carriers for pheromones and other olfactory cues emitted by the host. In particular, we have analysed forelegs, mouthparts (palps, chelicera and hypostome) and the second pair of legs (as control tissue) in reproductive and phoretic stages of the Varroa life cycle. We identified 958 Varroa proteins, most of them common to the different organs and stages. Sequence analysis shows that four proteins can be assigned to the odorant-binding protein (OBP)-like class, which bear some similarity to insect OBPs, but so far have only been reported in some Chelicerata...
April 10, 2018: Journal of Proteomics
Hala M Ayoub, Mary Ruth McDonald, James Alan Sullivan, Rong Tsao, Kelly A Meckling
Metabolic Syndrome (MetS) is a complex disorder that predisposes an individual to Cardiovascular Diseases and type 2 Diabetes Mellitus. Proteomics and bioinformatics have proven to be an effective tool to study complex diseases and mechanisms of action of nutrients. We previously showed that substitution of the majority of carbohydrate in a high fat diet by purple potatoes (PP) or purple carrots (PC) improved insulin sensitivity and hypertension in an animal model of MetS (obese Zucker rats) compared to a control sucrose-rich diet...
April 6, 2018: Nutrients
Rieko Oyama, Fusako Kito, Marimu Sakumoto, Kumiko Shiozawa, Shunichi Toki, Makoto Endo, Akihiko Yoshida, Akira Kawai, Tadashi Kondo
Synovial sarcoma is an aggressive mesenchymal tumor, characterized by the presence of unique transfusion gene, SS18-SSX. Cell lines enable researchers to investigate the molecular backgrounds of disease and the significance of SS18-SSX in relevant cellular contexts. We report the establishment and proteomic characterization of a novel synovial sarcoma cell line. Primary tissue culture was performed using tumor tissue of synovial sarcoma. The established cell line was authenticated by assessing its DNA microsatellite short tandem repeat analysis and characterized by in vitro assay...
April 6, 2018: In Vitro Cellular & Developmental Biology. Animal
Katarína Furmanová, Jan Byška, Eduard M Gröller, Ivan Viola, Jan J Paleček, Barbora Kozlíková
BACKGROUND: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space...
April 6, 2018: BMC Bioinformatics
Tiao-Lai Huang, Li-Hua Lo
The proteomics approach is the new mantra in disease biomarker research in areas such as major depression (MD). Current protocols for investigating biomarkers in biological fluid often employ both immuno-based and non-immuno-based technologies. The immuno-based method is used normally in measuring well-known disease biomarkers, and commercial kits are often available. Immuno-based methods such as radio-immunoassay and enzyme-linked immunosorbent assay are sensitive and specific. However, tedious sample preparations such as filtration and centrifugation are required...
April 3, 2018: Current Drug Metabolism
Anna Kwiecińska, Anna Porwit, Nazariy Souchelnytskyi, Ann Kaufeldt, Catharina Larsson, Svetlana Bajalica-Lagercrantz, Serhiy Souchelnytskyi
OBJECTIVE: The aim of this study was to identify differences in proteome profiles of diffuse large B-cell lymphoma (DLBCL) of nongerminal center (non-GC) versus GC type in the search for new markers and drug targets. METHODS: Six DLBCL, with 3 repeats for each, were used for the initial study by proteomics: 3 non-GC and 3 GC DLBCL cases. For immunohistochemistry, tissue microarrays were made from 31 DLBCL samples: 16 non-GC de novo lymphomas and 15 GC cases (11 transformed from follicular lymphomas and 4 de novo GC lymphomas)...
April 4, 2018: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
Meritxell Navarro-Reig, Carmen Bedia, Romà Tauler, Joaquim Jaumot
The increasing complexity of omics research has encouraged the development of new instrumental technologies able to deal with these challenging samples. In this way, the rise of multidimensional separations should be highlighted due to the massive amounts of information that provide with an enhanced analyte determination. Both proteomics and metabolomics benefit from this higher separation capacity achieved when different chromatographic dimensions are combined, either in LC or GC. However, this vast quantity of experimental information requires the application of chemometric data analysis strategies to retrieve this hidden knowledge, especially in the case of non-targeted studies...
April 3, 2018: Proteomics
Benjamin E Rubin, TuAnh Ngoc Huynh, David G Welkie, Spencer Diamond, Ryan Simkovsky, Emily C Pierce, Arnaud Taton, Laura C Lowe, Jenny J Lee, Scott A Rifkin, Joshua J Woodward, Susan S Golden
The broadly conserved signaling nucleotide cyclic di-adenosine monophosphate (c-di-AMP) is essential for viability in most bacteria where it has been studied. However, characterization of the cellular functions and metabolism of c-di-AMP has largely been confined to the class Bacilli, limiting our functional understanding of the molecule among diverse phyla. We identified the cyclase responsible for c-di-AMP synthesis and characterized the molecule's role in survival of darkness in the model photosynthetic cyanobacterium Synechococcus elongatus PCC 7942...
April 2, 2018: PLoS Genetics
Ryan Peckner, Samuel A Myers, Alvaro Sebastian Vaca Jacome, Jarrett D Egertson, Jennifer G Abelin, Michael J MacCoss, Steven A Carr, Jacob D Jaffe
Mass spectrometry with data-independent acquisition (DIA) is a promising method to improve the comprehensiveness and reproducibility of targeted and discovery proteomics, in theory by systematically measuring all peptide precursors in a biological sample. However, the analytical challenges involved in discriminating between peptides with similar sequences in convoluted spectra have limited its applicability in important cases, such as the detection of single-nucleotide polymorphisms (SNPs) and alternative site localizations in phosphoproteomics data...
April 2, 2018: Nature Methods
John T Halloran, David M Rocke
Percolator is an important tool for greatly improving the results of a database search and subsequent downstream analysis. Using support vector machines (SVMs), Percolator recalibrates peptide-spectrum matches based on the learned decision boundary between targets and decoys. To improve analysis time for large-scale data sets, we update Percolator's SVM learning engine through software and algorithmic optimizations rather than heuristic approaches that necessitate the careful study of their impact on learned parameters across different search settings and data sets...
April 6, 2018: Journal of Proteome Research
Simone Albrecht, Christian Kaisermayer, David Reinhart, Monica Ambrose, Renate Kunert, Anna Lindeberg, Jonathan Bones
The monitoring of protein biomarkers for the early prediction of cell stress and death is a valuable tool for process characterization and efficient biomanufacturing control. A representative set of six proteins, namely GPDH, PRDX1, LGALS1, CFL1, TAGLN2 and MDH, which were identified in a previous CHO-K1 cell death model using discovery LC-MSE was translated into a targeted liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM-MS) platform and verified. The universality of the markers was confirmed in a cell growth model for which three Chinese hamster ovary host cell lines (CHO-K1, CHO-S, CHO-DG44) were grown in batch culture in two different types of basal media...
April 2, 2018: Analytical and Bioanalytical Chemistry
Shulin Chen, Juan Chen, Fu Hou, Yigao Feng, Ruiqi Zhang
BACKGROUND: Spike architecture mutants in tetraploid wheat (Triticum turgidum L., 2n = 28, AABB) have a distinct morphology, with parts of the rachis node producing lateral meristems that develop into ramified spikelete (RSs) or four-rowed spikelete (FRSs). The genetic basis of RSs and FRSs has been analyzed, but little is known about the underlying developmental mechanisms of the lateral meristem. We used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a quantitative proteomic analysis of immature spikes harvested from tetraploid near-isogenic lines of wheat with normal spikelete (NSs), FRSs, and RSs and investigated the molecular mechanisms of lateral meristem differentiation and development...
April 2, 2018: BMC Genomics
Farsad Afshinnia, Thekkelnaycke M Rajendiran, Stefanie Wernisch, Tanu Soni, Adil Jadoon, Alla Karnovsky, George Michailidis, Subramaniam Pennathur
Technological advances in mass spectrometry-based lipidomic platforms have provided the opportunity for comprehensive profiling of lipids in biological samples and shown alterations in the lipidome that occur in metabolic disorders. A lipidomic approach serves as a powerful tool for biomarker discovery and gaining insight to molecular mechanisms of disease, especially when integrated with other -omics platforms (ie, transcriptomics, proteomics, and metabolomics) in the context of systems biology. In this review, we describe the workflow commonly applied to the conduct of lipidomic studies including important aspects of study design, sample preparation, biomarker identification and quantification, and data processing and analysis, as well as crucial considerations in clinical applications...
March 2018: Seminars in Nephrology
Aylin Kanli, Murat Kasap, Kubra K Yoneten, Gurler Akpinar, Mehmet Dogan Gulkac
Tetracycline regulated protein expression in mammalian cells is a powerful tool to predict the physiological function, cellular localization, and stability of a protein. In addition, to predict metabolic networks affected by the expression of wild-type or mutant forms of proteins, researchers generally produce a single mammalian cell clone that can express the protein of interest under tetracycline control and study the changes occurring in overall proteome before and after expression of a protein of interest...
March 30, 2018: Journal of Cellular Biochemistry
Ivana Perić, Victor Costina, Andrijana Stanisavljević, Peter Findeisen, Dragana Filipović
Due to the severity of depressive symptoms, there remains a necessity in defining the underlying mechanisms of depression and the precise actions of antidepressants in alleviating these symptoms. Proteomics is a powerful and promising tool for discovering novel pathways of cellular responses to disease and treatment. As chronic social isolation (CSIS) is a valuable animal model for studying depression, we performed a comparative subproteomic study of rat hippocampus to explore the effect of six weeks of CSIS and the therapeutic effect of chronic fluoxetine (Flx) treatment (last three weeks of CSIS; 15 mg/kg/day)...
March 26, 2018: Neuropharmacology
Veronika Suni, Tomi Suomi, Tomoya Tsubosaka, Susumu Y Imanishi, Laura L Elo, Garry L Corthals
Motivation: Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments...
March 27, 2018: Bioinformatics
Jeerang Wongtrakul, Chonticha Saisawang, Benjawan Kumrapich, Jiraprapa Wipasa, Sittiruk Roytrakul, Albert J Ketterman
Parkinson's disease is the second most common neurodegenerative disorder after Alzheimer's disease. The disease is associated with dopaminergic neuron losses in the substantia nigra area of the brain and the formation of cytoplasmic inclusion bodies. Human glutathione transferase omega 1 (hGSTO1) appears to have a role in modulating stress response. The study was aimed to elucidate differentially expressed proteins caused by oxidative stress induced by 6-hydroxydopamine (6-OHDA). Human neuronal cells SH-SY5Y overexpressing hGSTO1 were used to investigate protein glutathionylation and the modulation of cellular protein expression...
March 2018: General Physiology and Biophysics
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