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Tifications made by MS/MS and database search. Anal Chem. 2002;74:5383?2. 93. Nesvizhskii
Tifications made by MS/MS and database search. Anal Chem. 2002;74:5383?2. 93. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003;75:4646?8. 94. Searle BC, Turner M, Nesvizhskii AI. Improving sensitivity by Pentetreotide probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res. 2008;7:245?3. 95. Gokce E, Shuford CM, Franck WL, Dean RA, Muddiman DC. Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows. J Am Soc Mass Spectrom. 2011;22:2199?08.Tsolis et al. Clinical Proteomics (2015) 12:Page 16 of96. Camargo A, Azuaje F, Wang H, Zheng H. Permutation - based statistical tests for multiple hypotheses. Source Code Biol Med. 2008;3:15. 97. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091?. 98. Shannon P, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23633924 Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498?04.Submit your next manuscript to BioMed Central and take full advantage of:?Convenient online submission ?Thorough peer review ?No space constraints or color figure charges ?Immediate publication on acceptance ?Inclusion in PubMed, CAS, Scopus and Google Scholar ?Research which is freely available for redistributionSubmit your manuscript at www.biomedcentral.com/submit
Hayashi et al. Clin Proteom (2015) 12:20 DOI 10.1186/s12014-015-9091-RESEARCHOpen AccessA proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritisJunji Hayashi1, Makoto Kihara2, Harubumi Kato1,3 and Toshihide Nishimura3*Abstract Background: Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear. Regardless of numerous investigations of RA by means of genomic and proteomic approaches, proteins interplaying in RA synovial tissues that contain various types of synoviocytes, are not yet sufficiently understood. Hence we have conducted an HPLC/mass spectrometry-based exploratory proteomic analysis focusing on synoviocyte lesions laser-microdissected (LMD) from formalin-fixed paraffin-embedded (FFPE) synovial tissues (RA, n = 15; OA, n = 5), where those of Osteoarthritis (OA) were used as the control. Results: A total of 508 proteins were identified from the RA and OA groups. With PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/24059235 the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (RSC) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues. These include stromelysin-1 (MMP3), proteins S100-A8 and S100-A9, plastin-2, galectin-3, calreticulin, cathepsin Z, HLA-A, HLA-DRB1, ferritin, neutrophil defensin 1, CD14, MMP9 etc. Conclusions: Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1. Net.
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