Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

• DOI: 10.1074/mcp.ra117.000543
• Publication Date: 2018-02-28T01:35:22Z
• Authors: Vagisha Sharma; Josh Eckels; Birgit Schilling; Christina Ludwig; Jacob D. Jaffe; Michael J. MacCoss; Brendan MacLean
• Keywords: Skyline; Panorama

To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers readers immediate visual access data behind conclusions, we present Panorama Public (https://panoramaweb.org/public.url), repository Skyline documents supporting results. is built on Panorama, an open source management system mass spectrometry targeted environment. The web application facilitates viewing, sharing, disseminating contained in via web-browser. users can easily upload their server allow other researchers explore uploaded web-interface through variety familiar summary graphs as well annotated views chromatographic peaks Skyline. This makes ideal sharing targeted, quantitative collaborators, reviewers, larger proteomics community. employs full visualization capabilities which during manuscript review. (1.MacLean B. Tomazela D.M. Shulman N. Chambers M. Finney G.L. Frewen Kern R. Tabb D.L. Liebler D.C. MacCoss M.J. Skyline: document editor creating analyzing experiments.Bioinformatics. 2010; 26: 966-968Crossref PubMed Scopus (2963) Google Scholar) widely used software tool processing from range acquisition techniques such selected reaction monitoring (SRM) 1The abbreviations are: SRM, monitoring; DDA, data-dependent acquisition; PRM, parallel DIA, data-independent AUC, area under curve; PASSEL, PeptideAtlas SRM Experiment Library; MCP, Molecular & Cellular Proteomics. Proteomics., (DDA) (2.Schilling Rardin MacLean B.X. Zawadzka A.M. B.E. Cusack M.P. Sorensen D.J. Bereman M.S. Jing E. Wu C.C. Verdin Kahn C.R. Maccoss Gibson B.W. Platform-independent label-free quantitation proteomic using MS1 extracted ion chromatograms skyline: protein acetylation phosphorylation.Mol. Cell. 2012; 11: 202-214Abstract Full Text PDF (334) Scholar), (PRM) (3.Schilling Held J.M. Sahu A.K. Peters T. Wolfe A.J. Hunter C.L. Multiplexed, scheduled, high-resolution scan QqTOF instrument integrated spectrometric workflows.Anal. Chem. 2015; 87: 10222-10229Crossref (74) Scholar, 4.Sherrod S.D. Myers M.V. Li J.S. Carpenter K.L. Maclean Ham A.-J.L. Label-free modifications by pseudo internal reference peptides.J. Proteome Res. 3467-3479Crossref (57) (DIA) (5.Egertson J.D. Johnson Xuan Y. Multiplexed peptide analysis Skyline.Nat. Protoc. 10: 887-903Crossref (134) Scholar). A key strength its that include vast array interactive interrogating underlying data. (6.Sharma V. Eckels J. Taylor G.K. N.J. Stergachis A.B. Joyner S.A. Yan P. Whiteaker J.R. Halusa G.N. Schilling Colangelo C.M. Paulovich A.G. Carr Jaffe Panorama: knowledge base.J. 2014; 13: 4205-4210Crossref (147) implements several graphs, including chromatogram are critical evaluating quality These enable viewers get quick overview within web-browser, without having or even needing install Combined ability click button this documents. Additionally, original also be downloaded opened making dissemination easier aiding reproducing Many laboratories organizations use Skyline-processed For lacking resources inclination set up own have made available hosted Department Genome Sciences at University Washington called PanoramaWeb (https://panoramaweb.org). all storing securely experimental Since introduction 2013, has become popular choice among who process As February 2018, hosts 283 different (https://panoramaweb.org/dashboard.url). Researchers request free projects laboratory organization PanoramaWeb, given administrative control over project space. includes organize folders configure each folder researchers. Several flexibility host associated research manuscripts PanoramaWeb. They provided journals login while being reviewed then public once was accepted publication. Although enabled user projects, capability exposed some shortcomings. Because dispersed it not possible searchable location manner authors retain difficult guarantee continued availability exactly they were originally published. addresses first concern central, explored same interface visualizing We simple mechanism copying Public. second concern, Public, cannot modified remains form, permanent location. review keeping private process, anonymous secure reviewers. On notification paper been publication publicly accessible. Existing repositories, Library (PASSEL) (7.Farrah Deutsch E.W. Kreisberg Sun Z. Campbell D.S. Mendoza L. Kusebauch U. Brusniak M.-Y. Hüttenhain Schiess Selevsek Aebersold Moritz R.L. PASSEL: SRMexperiment library.Proteomics. 12: 1170-1175Crossref (167) experiments. However, PASSEL only requires submit transition lists describing analytes and, optionally, output tools analysis. Accompanying raw submitted reprocessed uniform view PASSEL. loses any tool-specific information creates disconnect between re-processed viewing interface. Unless tool, another means visualization, insight into how chosen performed peak picking. It assess reliability curve (AUC) numbers around based now requirement recently Proteomics (MCP) guidelines experiments (8.Abbatiello S. Ackermann B.L. Borchers C. Bradshaw R.A. Chalkley Choi Domon Hoofnagle A.N. Keshishian H. Kuhn Mani D. Neubert Smith Vitek O. Zimmerman New development measurements peptides proteins.Mol. 2017; 16: 327-328Abstract (32) Support uploading since version 1.4 (released 11/12/2012). current website (https://skyline.ms). must If does already new requested filling form page: https://panoramaweb.org/signup.url. Before one-time configuration step required setup server. After initial setup, clicking More details found introductory tutorial supplementary Note S1. In addition documents, may information, figures tables enhance presentation context work. offers add additional content images result files create custom dynamic analyses Users customized micro-website covering more detailed aspects preparing submission building included S2. Once snapshot copied (Fig. 1). handled administrators week. immediately kept submitting developed interest sets suitable approaches DDA DIA. Fig. 1 describes workflow 1, prepare description experiment where enter abstract, sample descriptions, organism(s) studied, instrument(s) collect step2). related complete 3 workflow, clicks 2A) resulting link 2B) choose name relevant data, memorable. becomes referenced papers. check box 2C) private. option appropriate when will journal peer checked, reviewer account read-only submitter after When created identical respects folder. page components layout 3). edited authors. make updates feedback, changes update common added important efficient journal. Requests copy existing administrators. receiving request, initiate successful completion send confirmation E-mail keep checked E-mail. Authors relay these editors submission. While review, browsing experience presented Panorama. Reviewers along either web-browser directly download them computer. Within list marked boundaries analyte replicates 4). Chromatograms light heavy isotopically labeled single replicate displayed side-by-side comparison. number independent steadily launch 2013. labs. implemented early 2015. There 71 13,000 800 requests representing broad geographical distribution (https://panoramaweb.org/public-usage.url). summary, provides intended central Access managed required. requested, process. Data accessible Open published, useful specifically designed publishing generated Skyline-based workflows, public. - end-to-end support MCP (http://www.mcponline.org/site/misc/MCP_Targeted_Mass_Spec_Guidelines_1.27.17.pdf), publications supported. Results point-and-click operation studies. Tools let entirety protect against accidental deletion alteration. browse conclusions interrogation reprocessing features Readers visibility actual calculating areas help evaluate reported hope simplicity quickly browser encourage share Download .pdf (2.26 MB) Help pdf