EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-06DOI: 10.1016/j.euprot.2015.07.008
Geisa P.C. Evaristo , Martijn W.H. Pinkse , Tianbao Chen , Lei Wang , Shabaz Mohammed , Albert J.R. Heck , Isabella Mathes , Friedrich Lottspeich , Chris Shaw , Juan Pablo Albar , Peter D.E.M. Verhaert
{"title":"De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri","authors":"Geisa P.C. Evaristo , Martijn W.H. Pinkse , Tianbao Chen , Lei Wang , Shabaz Mohammed , Albert J.R. Heck , Isabella Mathes , Friedrich Lottspeich , Chris Shaw , Juan Pablo Albar , Peter D.E.M. Verhaert","doi":"10.1016/j.euprot.2015.07.008","DOIUrl":"10.1016/j.euprot.2015.07.008","url":null,"abstract":"<div><p>An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (<em>Odorrana schmackeri</em>) skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. <em>De novo</em> sequencing was achieved by complementary CID and ETD fragmentations of full-length peptides and of selected tryptic fragments. Heavy and light isotope dimethyl labeling assisted with annotation of sequence ion series. The identified primary structures are GCD[I/L]STCATHN[I/L]VNE[I/L]NKFDKSKPSSGGVGPESP-NH<sub>2</sub> and SCNLSTCATHNLVNELNKFDKSKPSSGGVGPESF-NH<sub>2</sub>, i.e. two carboxyamidated 34 residue peptides with an aminoterminal intramolecular ring structure formed by a disulfide bridge between Cys<sub>2</sub> and Cys<sub>7</sub>. Edman degradation analysis of the second peptide positively confirmed the exact sequence, resolving I/L discriminations. Both peptide sequences are novel and share homology with calcitonin, calcitonin gene related peptide (CGRP) and adrenomedullin from other vertebrates. Detailed sequence analysis as well as the 34 residue length of both <em>O. schmackeri</em> peptides, suggest they do not fully qualify as either calcitonins (32 residues) or CGRPs (37 amino acids) and may justify their classification in a novel peptide family within the calcitonin gene related peptide superfamily. Smooth muscle contractility assays with synthetic replicas of the S–S linked peptides on rat tail artery, uterus, bladder and ileum did not reveal myotropic activity.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 157-166"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-05-08DOI: 10.1016/j.euprot.2015.04.003
Francesco Finamore , Feliciano Priego-Capote , Severine Nolli , Pierre Fontana , Jean-Charles Sanchez
{"title":"Aspirin-mediated acetylation of haemoglobin increases in presence of high glucose concentration and decreases protein glycation","authors":"Francesco Finamore , Feliciano Priego-Capote , Severine Nolli , Pierre Fontana , Jean-Charles Sanchez","doi":"10.1016/j.euprot.2015.04.003","DOIUrl":"10.1016/j.euprot.2015.04.003","url":null,"abstract":"<div><p>Glycation represents the first stage in the development of diabetic complications. Aspirin was shown to prevent sugars reacting with proteins, but the exact mechanism of this interaction was not well defined. We performed a quantitative analysis to calculate the levels of acetylation and glycation of haemoglobin, among others red blood cell (RBC) proteins, using a label free approach. After glucose incubation, increases in the acetylation levels were seen for several haemoglobin subunits, while a parallel decrease of their glycation levels was observed after aspirin incubation. These results suggest that, a mutual influence between these two modifications, occur at protein level.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 116-127"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.04.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54256891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-02DOI: 10.1016/j.euprot.2015.06.004
Harish R. Cheruku , Abidali Mohamedali , David I. Cantor , Sock Hwee Tan , Edouard C. Nice , Mark S. Baker
{"title":"Transforming growth factor-β, MAPK and Wnt signaling interactions in colorectal cancer","authors":"Harish R. Cheruku , Abidali Mohamedali , David I. Cantor , Sock Hwee Tan , Edouard C. Nice , Mark S. Baker","doi":"10.1016/j.euprot.2015.06.004","DOIUrl":"10.1016/j.euprot.2015.06.004","url":null,"abstract":"<div><p>In non-cancerous cells, transforming growth factor-β (TGFβ) regulates cellular responses primarily through Smad signaling. However, during cancer progression (including colorectal) TGFβ promotes tumoral growth via Smad-independent mechanisms and is involved in crosstalk with various pathways like the mitogen-activated protein kinases (MAPK) and Wnt. Crosstalk between these pathways following activation by TGFβ and subsequent downstream signaling activity can be referred to as a crosstalk signaling signature. This review highlights the progress in understanding TGFβ signaling crosstalk involving various MAPK pathway members (e.g., extracellular signal-regulated kinase (Erk) 1/2, Ras, c-Jun N-terminal kinases (JNK) and p38) and the Wnt signaling pathway.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 104-115"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-06-06DOI: 10.1016/j.euprot.2015.05.006
Rafael D. Melani , Gabriel D.T. Araujo , Paulo C. Carvalho , Livia Goto , Fábio C.S. Nogueira , Magno Junqueira , Gilberto B. Domont
{"title":"Seeing beyond the tip of the iceberg: A deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus","authors":"Rafael D. Melani , Gabriel D.T. Araujo , Paulo C. Carvalho , Livia Goto , Fábio C.S. Nogueira , Magno Junqueira , Gilberto B. Domont","doi":"10.1016/j.euprot.2015.05.006","DOIUrl":"10.1016/j.euprot.2015.05.006","url":null,"abstract":"<div><p>The complete characterization of the snake venom protein components is a requirement for a systems-wide understanding of their biological context. In this work, we provide a deep proteomic characterization of <em>Crotalus durissus terrificus</em> venom using different bottom-up approaches. We identified more than five times more protein families than the sum of all identifications previously reported. For the first time in this sub-species, we report the identification of three new toxin families: CRISP, phospholipase-B, and SVVEGF. This work also describes proteins involved in regulation of toxin synthesis and processing that are present in venom.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 144-156"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.05.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-07DOI: 10.1016/j.euprot.2015.06.006
Norelle C. Wildburger , Cheryl F. Lichti , Richard D. LeDuc , Mary Schmidt , Roger A. Kroes , Joseph R. Moskal , Carol L. Nilsson
{"title":"Quantitative proteomics and transcriptomics reveals metabolic differences in attracting and non-attracting human-in-mouse glioma stem cell xenografts and stromal cells","authors":"Norelle C. Wildburger , Cheryl F. Lichti , Richard D. LeDuc , Mary Schmidt , Roger A. Kroes , Joseph R. Moskal , Carol L. Nilsson","doi":"10.1016/j.euprot.2015.06.006","DOIUrl":"10.1016/j.euprot.2015.06.006","url":null,"abstract":"<div><p>Bone marrow-derived human mesenchymal stem cells (BM-hMSCs) show promise as cell-based delivery vehicles for anti-glioma therapeutics, due to innate tropism for gliomas. However, in clinically relevant human-in-mouse glioma stem cell xenograft models, BM-hMSCs tropism is variable. We compared the proteomic profile of cancer and stromal cells in GSCXs that attract BM-hMSCs (“attractors”) with those to do not (“non-attractors”) to identify pathways that may modulate BM-hMSC homing, followed by targeted transcriptomics. The results provide the first link between fatty acid metabolism, glucose metabolism, ROS, and N-glycosylation patterns in attractors. Reciprocal expression of these pathways in the stromal cells suggests microenvironmental cross-talk.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 94-103"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-06-11DOI: 10.1016/j.euprot.2015.06.001
Andrew J. Percy , Jessica Tamura-Wells , Juan Pablo Albar , Kerman Aloria , Ardeshir Amirkhani , Gabriel D.T. Araujo , Jesus M. Arizmendi , Francisco J. Blanco , Francesc Canals , Jin-Young Cho , Núria Colomé-Calls , Fernando J. Corrales , Gilberto Domont , Guadalupe Espadas , Patricia Fernandez-Puente , Concha Gil , Paul A. Haynes , Maria Luisa Hernáez , Jin Young Kim , Arthur Kopylov , Christoph H. Borchers
{"title":"Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment","authors":"Andrew J. Percy , Jessica Tamura-Wells , Juan Pablo Albar , Kerman Aloria , Ardeshir Amirkhani , Gabriel D.T. Araujo , Jesus M. Arizmendi , Francisco J. Blanco , Francesc Canals , Jin-Young Cho , Núria Colomé-Calls , Fernando J. Corrales , Gilberto Domont , Guadalupe Espadas , Patricia Fernandez-Puente , Concha Gil , Paul A. Haynes , Maria Luisa Hernáez , Jin Young Kim , Arthur Kopylov , Christoph H. Borchers","doi":"10.1016/j.euprot.2015.06.001","DOIUrl":"10.1016/j.euprot.2015.06.001","url":null,"abstract":"<div><p>The reproducibility of plasma protein quantitation between laboratories and between instrument types was examined in a large-scale international study involving 16 laboratories and 19 LC–MS/MS platforms, using two kits designed to evaluate instrument performance and one kit designed to evaluate the entire bottom-up workflow. There was little effect of instrument type on the quality of the results, demonstrating the robustness of LC/MRM-MS with isotopically labeled standards. Technician skill was a factor, as errors in sample preparation and sub-optimal LC–MS performance were evident. This highlights the importance of proper training and routine quality control before quantitation is done on patient samples.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 6-15"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-29DOI: 10.1016/j.euprot.2015.07.016
Concha Gil, Fernando Corrales, Garry Corthals, György Marko-Varga, Peter Verhaert
{"title":"EuPA’s tribute to Juan Pablo Albar","authors":"Concha Gil, Fernando Corrales, Garry Corthals, György Marko-Varga, Peter Verhaert","doi":"10.1016/j.euprot.2015.07.016","DOIUrl":"10.1016/j.euprot.2015.07.016","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 1-5"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-29DOI: 10.1016/j.euprot.2015.07.014
Kenneth Verheggen , Lennart Martens
{"title":"Ten years of public proteomics data: How things have evolved, and where the next ten years should lead us","authors":"Kenneth Verheggen , Lennart Martens","doi":"10.1016/j.euprot.2015.07.014","DOIUrl":"10.1016/j.euprot.2015.07.014","url":null,"abstract":"<div><p>Ten years ago, the first public proteomics repositories became available online. This anniversary is therefore an excellent occasion to look back on the past decade and evaluate what has changed in this time period. At the same time however, one should also dare to look forward, and therefore prepare for the next 10 years of proteomics data sharing.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 28-35"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-07-15DOI: 10.1016/j.euprot.2015.07.013
Stefan Bugovsky , Wolfgang Winkler , Werner Balika , Günter Allmaier
{"title":"Long time storage (archiving) of peptide, protein and tryptic digest samples on disposable nano-coated polymer targets for MALDI MS","authors":"Stefan Bugovsky , Wolfgang Winkler , Werner Balika , Günter Allmaier","doi":"10.1016/j.euprot.2015.07.013","DOIUrl":"10.1016/j.euprot.2015.07.013","url":null,"abstract":"<div><p>Archiving of biological specimens is important due to the importance of reanalysis of already prepared MALDI MS samples or simultaneuous analysis of a sample series. Proteins/peptides and digests were prepared for measurement on a polymer-based metal nano-coated MALDI target and subjected to various storage conditions (−80<!--> <!-->°C to RT) in a vacuum-sealed pouch and at atmosphere for 6 months. The MS data gathered from these preparations illustrate trends in the aging of different samples and to find optimal storage conditions (−20 or −80<!--> <!-->°C in low oxygen environment). The disposable/low cost target proved to be a suitable platform for storage and MALDI MS.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 48-54"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EuPA Open ProteomicsPub Date : 2015-09-01Epub Date: 2015-05-06DOI: 10.1016/j.euprot.2015.04.002
Vital Vialas , Concha Gil
{"title":"Proteopathogen2, a database and web tool to store and display proteomics identification results in the mzIdentML standard","authors":"Vital Vialas , Concha Gil","doi":"10.1016/j.euprot.2015.04.002","DOIUrl":"10.1016/j.euprot.2015.04.002","url":null,"abstract":"<div><p>The Proteopathogen database was the first proteomics online resource focused on experiments related to <em>Candida albicans</em> and other fungal pathogens and their interaction with the host. Since then, the HUPO-PSI standards were implemented and settled, and the first large scale <em>C. albicans</em> proteomics resource appeared as a <em>C. albicans</em> PeptideAltas. This has enabled the remodeling of Proteopathogen to take advantage and benefit from the use of the HUPO-PSI adopted format for peptide and protein identification mzIdentML and continue offering a centralized resource for <em>C. albicans</em>, other fungal pathogens and different cell lines proteomics data.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 22-27"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54256876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}