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High throughput discovery of protein variants using proteomics informed by transcriptomics

Proteomics informed by transcriptomics (PIT), in which proteomic MS/MS spectra are searched against open reading frames derived from de novo assembled transcripts, can reveal previously unknown ... (proteomics informed by transcriptomics) methodology in which spectra acquired from liquid chromatography tandem mass spectrometry (LC–MS/MS) proteomics are searched against open reading frames (ORFs) derived

Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii

metabolism and storage occur in plastoglobuli. Functions of each of these compartments have been elucidated by proteomics; i.e. the use of mass spectrometry and bioinformatics to carry out large scale ... , photographed and then dried. 35S-labelled proteins were revealed by phosphorimaging. 5 / 20 Mass spectrometry Proteomics grade endoproteinases (Lys-C and Trypsin Gold) and ProteaseMax surfactant were purchased

Proteomics and transcriptomics analyses of ataxia telangiectasia cells treated with Dexamethasone

staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis . Proteomics 1 : 1359 ± 1363 . https://doi.org/10.1002/ 1615 - 9861 ... 77 : 1137 ± 1142 . https://doi.org/10.1292/jvms.14-0651 PMID: 25947323 54. Cheema AK , Varghese RS , Timofeeva O , Zhang L , Kirilyuk A , Zandkarimi F , et al. ( 2013 ) Functional proteomics analysis

Salivary proteomics of healthy dogs: An in depth catalog

Wolfhound (1), Jack Russell Terrier (1), Mixed breed dog (1), Newfoundland (1), and Scottish Deerhound (1) (Fig 1). To try to investigate the potential effect of genetic lineage on the salivary proteomics ... protein data from the dog saliva was measured via protein spectral counts from the MS-based proteomics data. Normalized spectral counts were assigned to each 5 / 16 identified protein using the

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics

‑ values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal ... available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html. Peptide identification; Protein identification; Proteomics; Tandem mass spectrometry Introduction RAId is a

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases

) of 9-12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to ... might serve as treatment targets or as predictive markers for these kinds of metastasis. BRAF mutation; Cerebral melanoma metastases; Drug resistance; Melanoma; MAP kinase inhibitor; Proteomics

Identification of blood biomarkers in glioblastoma by SWATH mass spectrometry and quantitative targeted absolute proteomics

targeted absolute proteomics analysis. As a result, we identified eight biomarker candidates for GBM (leucine-rich alpha-2-glycoprotein (LRG1), complement component C9 (C9), C-reactive protein (CRP), alpha-1 ... fragment ion data sets [ 19 ]. SWATH-MS analysis offers several advantages, including high reproducibility and reliability of quantitative information, in discovery proteomics [ 20,21 ]. However, it has

Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

DTR protocol as a viable and straightforward alternative to the FASP protocol for proteomicsbased clinical research. Mass spectrometry; Proteomics; Label-free quantitation; FFPE; Archival tissue; FASP ... mass spectrometry based shot-gun proteomics [ 6–14 ]. This represents a significant leap forward in clinical proteomics. For a long time the highly crosslinked FFPE tissue specimens were considered to

Label free quantitative proteomics reveals the role of miR-200b in androgen-independent prostate cancer cells

studies indicated that miR‑ 200b inhibits the growth of androgen‑ independent prostate cancer (AIPC) cells. In this study, we employed quantitative proteomics techniques to unravel the role of miR‑ 200b in ... were analyzed by label‑ free proteomics. PANTHER was applied to analyze biological processes, molecular functions and pathways of proteins regulated by miR‑ 200b. miRBase was used to evaluate target

Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry—Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS

Hotel in Clearwater Beach, FL. The topic of the conference was BPeptidomics: Bridging the Gap between Proteomics and Metabolomics by Mass Spectrometry^. Peptidomics is the characterization and study of ... MS confirmation. The final presentation in this session was given by Marshall Bern (Protein Metrics) on BBacterial Peptidoglycan Analysis using a Proteomics Search Engine^. He presented the use of

Proteomics analysis identified peroxiredoxin 2 involved in early-phase left ventricular impairment in hamsters with cardiomyopathy

myocardial proteins involved in early-phase cardiac impairment, using proteomics analysis. Using the two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) combined with MALDI-TOF/TOF tandem ... hamsters that might be involved in compensatory cardiac hypertrophy or cardiac dysfunction [ 9 ]. The field of proteomics provides a systematic approach for quantitative and qualitative mapping of the

Tetrazine ligation for chemical proteomics

Determining small molecule—target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding

Correction: Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus

PM , Kropinski AM , Zebrowska J , Janus L , Szemiako K , Czajkowska E , et al. ( 2018 ) Sequence, genome organization, annotation and proteomics of the thermophilic , 47 .7 -kb Geobacillus

Urine proteomics of primary membranous nephropathy using nanoscale liquid chromatography tandem mass spectrometry analysis

; Proteomics; Alpha-1-antitrypsin; Afamin Background Primary membranous nephropathy (PMN) is the most common cause of nephrotic syndrome in the adult population [ 1, 2 ] and it is one of the most common ... nephropathy [ 24 ]. However, proteomic analysis of PMN has been rarely studied, especially in urine. Our aim was to test urine proteomics as a non-invasive method for identification of new protein biomarkers

Change of ranibizumab-induced human vitreous protein profile in patients with proliferative diabetic retinopathy based on proteomics analysis

in immune response, platelet degranulation, complement activation etc., suggesting that the effects of VEGF are involved in these signaling pathways. Proteomics; Proliferative diabetic retinopathy ... pathophysiology of PDR and to identify DR-associated risk factors, a proteomics analysis was performed to compare vitreous protein profiles of DM patients with and without development of DR, and some studies

Quantitative proteomics of pomegranate varieties with contrasting seed hardness during seed development stages

seed hardness adds to the current knowledge base of the molecular basis of seed hardness development. Pomegranate; Seed hardness; Proteomics; Seed developmental stages; Gene expression Introduction ... , proteomics analysis was performed using two pomegranate varieties: the soft-seeded variety Tunisia and the hard-seeded variety Sanbai. Our findings may provide a useful genetic resource for further analyses on

Differential Proteomics for Distinguishing Ischemic Stroke from Controls: a Pilot Study of the SpecTRA Project

Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park 8 Division of Medical Sciences, University of Victoria , Victoria, BC V8W 2Y2 , Canada 9 Department of Research and ... -based MS in this area. Proteomics; Plasma proteins; Mass spectrometry; Stroke; Hematologic tests; Infarction Introduction In the management of acute cerebrovascular syndrome (ACVS) [1], the high

Colorectal cancer patients with different C-reactive protein levels and 5-year survival times can be differentiated with quantitative serum proteomics

: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008583 (http://proteomecentral ... specificity, which limits its usefulness [ 10, 11 ]. Proteomics is the study of the complete proteome of a biological sample, and proteomic techniques such as mass spectrometry are widely used to search for

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus

this manuscript, we describe the complete, annotated TP-84 genome sequence, show that the sequence is unrelated to other characterized bacteriophages and present an in-depth proteomics analysis. Results ... similarity to 4divÐa distal tail protein (ORF46) from Lactococcus phage TP901-1 (Table 1, Figs 3 and 5; S1 File). The well-studied, from a genetics and proteomics standpoint, thermophilic bacteriophage offers

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems