{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/chrom02.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/CLUS-03-11.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/CLUS-01.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Chrom01.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Search_Degraded_chrom02.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Search_SCG2.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/CLUS-03_12.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Search_Chrom01.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Search_CLUS-01-11.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/Search_Chrom02.xml"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD005314/analysis.baf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":259,"searchCount":0},"additional":{"labhead_mail":["c-hirtz@chu-montpellier.fr"],"submitter":["Pierre-Olivier SCHMIT"],"technology_type":["Mass Spectrometry","Top-down proteomics"],"disease":["Alzheimer's Disease"],"software":["Not available"],"submitter_keywords":["Csf","Alzheimer","Proteoforms"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD005314"],"tissue":["Cerebrospinal Fluid"],"sample_protocol":[". In this study, we have investigated the capacities of last-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples, have developed the tools to process the intact protein data in an existing label-free quantification pipeline, and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease in a proof-of concept study. Several proteoforms have been pointed out for their capacity to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease and have been characterized."],"repository":["Pride"],"quantification_method":["MS1 intensity based label-free quantification method"],"modification":["monohydroxylated residue","amidated residue"],"data_protocol":["LC-MS data processing Data Processing : LC-MS data were automatically processed (calibration, protein signal extraction with Dissect™, deconvolution and determination of monoisotopic masses with SNAP™, charge state filtering, similarity filtering, export of deconvoluted monoisotopic masses with corresponding retention time and intensities) in Data Analysis 4.2™ (Bruker Daltonik, Bremen, Germany). Singly charged compounds have been automatically excluded. Only the isotopically resolved compounds have been taken into account. LC-MS/MS data were automatically processed (calibration, creation of the LC-MS/MS compound list, deconvolution, export of XML list with deconvoluted parent ion and fragment spectra masses and intensities) in Data Analysis 4.2™ (Bruker Daltonik, Bremen, Germany) Statistical analyses were performed with Profile Analysis 2.1™ (Bruker Daltonics). The retention times, intensities and deconvoluted masses and retention times obtained for each compound from the Data Analysis processing have been used to generate the bucket table. The mass accuracy and retention time tolerance were set to 2 ppm and 0,5 (High Flow analysis) or 2 min (Low Flow analysis).Compounds sharing the same mass and retention time coordinates within those tolerances have been considered as similar. The bucket tables were built with all compounds present at least in 60% of one class, and the missing values were replaced by the average value of the bucket in the class the analysis belongs to. Intensities values were then normalized with the quantile normalization algorithm available in Profile Analysis. A student’s t-test was performed to reveal compounds that were capable of discriminating 2 classes (p-value <0.02). We then selected the compounds that were also discriminating in the absence of normalization and missing values replacement for the correlation with clinical data step. This analysis was performed with the MedCalc™ 12.1.4.0 software. LC MS/MS identifications. Identifications were done either manually with BioTools 3.2™ (Bruker Daltonik, Bremen, Germany) or automatically with Byonic™ (ProteinMetrics, SanCarlos, USA). With BioTools, the Top-Down Sequencing search functionality was used with Mascot 2.4(Matrix Science) to identify proteoforms with a partially unmodified sequence. When this approach did not suffice to identify the protein the designated proteoform originates from, a blast search that was performed after an initial tag determination. In both cases, the full characterization was then obtained by mutation/modification searches performed with the Sequence Editor functionality available in BioTools 3.2™."],"omics_type":["Proteomics"],"labhead":["Dr. Christophe Hirtz"],"instrument_platform":["impact II"],"labhead_affiliation":["Clinical Proteomic Platform CHU de Montpellier - Hôpital St. Eloi Institute of Regenerative Medicine - Biotherapy - IRMB 80, av A. Fliche, 34295 Montpellier Cedex 5"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["28855124 Schmit PO, Vialaret J, Wessels HJCT, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics. 2018 175:12-26 10.1016/j.jprot.2017.08.003"],"submitter_mail":["pierre-olivier.schmit@bruker.com"],"curator_keywords":["Biomedical"],"submitter_affiliation":["Bruker Daltonique S.A"],"pubmed_abstract":["Thanks to proteomics investigations, our vision of the role of different protein isoforms in the pathophysiology of diseases has largely evolved. The idea that protein biomarkers like tau, amyloid peptides, ApoE, cystatin, or neurogranin are represented in body fluids as single species is obviously over-simplified, as most proteins are present in different isoforms and subjected to numerous processing and post-translational modifications. Measuring the intact mass of proteins by MS has the advantage to provide information on the presence and relative amount of the different proteoforms. Such Top-Down approaches typically require a high degree of sample pre-fractionation to allow the MS system to deliver optimal performance in terms of dynamic range, mass accuracy and resolution. In clinical studies, however, the requirements for pre-analytical robustness and sample size large enough for statistical power restrict the routine use of a high degree of sample pre-fractionation. In this study, we have investigated the capacities of current-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease. Statistical analysis has shown that several proteoforms can be used to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease.