Abstract PanoramaWeb was developed with the goal to address the growing need for a community resource to store, share, analyze, and reuse mass spectrometry assays created and refined with the Skyline Windows Client via a web-browser. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. The Panorama Public repository makes use of the full data visualization capabilities of Panorama which facilitates disseminating results processed with Skyline upon publication. The website can provide reviewers and readers access to the data behind the published conclusions and improves the transparency of quantitative mass spectrometry assays. Additionally, PanoramaWeb is build on-top of LabKey Server, a biomedical research data management system. This makes PanoramaWeb an ideal resource for mass spectrometry and proteomics collaborative projects as there is infrastructure for sharing documents, wiki pages, message boards, and managing shared specimens etc. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. Types of questions that can be answered with PanoramaWeb: 1. Are there any existing proteomics experiments or quantitative assays that study my favorite protein? 2. Can I find the underlying RAW and processed mass spectrometry data generated in this paper I am reading? 3. How can I share experimental mass spectrometry details and method validation to colleagues who want to implement a specific assay? 4. Can I track instrument performance longitudinally? Presenter: Michael J. MacCoss, Ph.D. Professor of Genome Sciences, University of Washington Upcoming webinars schedule: https://dknet.org/about/webinar

1. PanoramaWeb: A Resource to Manage, Share,
and Collaborate on Quantitative Mass
Spectrometry Experiments
https://maccosslab.org
https://panoramaweb.org/
Michael MacCoss

2. Needs:
! Protein and Peptide centric
! Intuitive document editor graphical
interface
! Full undo/redo support
! Direct analysis of all vendor RAW MS
data without conversion.
! Ability to choose peptides and
transitions based on peptide spectrum
libraries
! Free and open source
! Developed and supported professionally
http://skyline.ms
Skyline:Vendor'Neutral'Development'of'Methods'and'Quantitative'Analysis

3. Panorama
• Started'in'2012:'9/year'partnership'with'LabKey'Software
• Designed'for'Sharing'Skyline'Documents'and'Associated'Data
• Free'hosted'version'(http://panoramaweb.org)
o 574'labs'hosted'(Including'CPTAC,'LINCS,'TPAD2,'TAMADOR,'ICPC)
o >24,710'Skyline'documents'uploaded'
o User'controlled'security
o Excellent'for'sharing'data'between'labs'and'the'public
• Publish'fully'annotated'Skyline'documents
o http://panoramaweb.org/public.url
o Part'of'ProteomeXchange
o 337'public'data'sets'(more'in'review)
o Reviewer'accessibility
• Locally'installable'server'application
Abbatiello,+et+al.+MCP+Guidelines,+2017
Sharma,+et+al.+J.#Proteome#Res.#2014
Sharma,+et+al.+MCP#2018

4. Publishing*to*Panorama

5. Sharma&2014 5

6. Growth'of'PanoramaWeb
Lab$Growth$to$574 Skyline$docs$to$24,712

7. Viewing'Runs'+ Peptides

8. Viewing'Proteins

9. Viewing'Peptides

10. Every&Change&to&the&Document&is&Tracked&in&the&Audit&Log
Fully%Internationalized:%Log%can%be%displayed%in%English,%Chinese%or%Japanese

11. Full$Audit$Log$and$Versioning$Tracked$in$Panorama
Getting'close'to'FDA'21'CFR'Part'11'compliance

12. Storing(and(Managing(Assay(Calibration/Validation(Data

13. AutoQC Facilitates.Longitudinal.Tracking
Bereman,(et.(al,(J.#Proteome#Res.#2016

14. System'Suitability'and'Process'Controls
System'
Suitability
Process'
Controls
PRTC'Peptides'
+'BSA'Digest
Yeast'Enolase PRTC'Peptides
Digestion
Added$to$Each$
Sample$to$
Assess$the$
Sample$Prep$
Sample$To$
Assess$System

15. System'Suitability'and'Process'Controls
System'
Suitability
Process'
Controls
PRTC'Peptides'
+'BSA'Digest
Yeast'Enolase PRTC'Peptides
Digestion

16. Assessing'the'System:'System'Suitability
• Stable'sample'that'doesn’t'change'with'
time'
• Similar'to'your'actual'samples'
o Small'molecule'
o Peptides'
o Proteins'
• Minimal'carryover'
• Inexpensive'
• Easy'to'prepare'
• Mixture'of'several'analytes'
• Commercially'available'and'QC’d'
We#Use:
• A"mix"of"Pierce"
Retention"Time"
Calibration
• Bovine"serum"
albumin"digested"in"
bulk
It#should#assess:
• That"peptide"intensities"
(precursor"and"product"
ions)"are"within"tolerated"
variance"over"time
• The"chromatographic"RT"
and"peak"shape"is"
acceptable
• Track"mass"accuracy

17. Assessing'the'System:'System'Suitability

18. Vendor'Neutral'AutoQC
Statistical(Process(Control
• System(Suitability
• Quality(Assurance
• Quality(Control

19. Data$Can$be$Tracked$Longitudinally$in$Panorama

20. Track&Performance&Overtime
0

21. System'Suitability'is'a'Lab'Wide'Folder:'
Tracking'&'Documenting'Performance'is'a'Requirement'of'Using'a'System

22. System'Suitability'and'Process'Controls
System'
Suitability
Process'
Controls
PRTC'Peptides'
+'BSA'Digest
Yeast'Enolase PRTC'Peptides
Digestion

23. Process'Controls'…'Assess'Process
Used%to%assess%steps%in%the%sample%
preparation%process.
• Examples:
• Digestion
• Solid8phase%extraction
• Peptide%loss
• We%spike%an%intact%protein%and%
peptides%into%each%sample
Process%
Controls
Yeast%Enolase PRTC%Peptides
Digestion
• If#something#happened#to#the#digestion
• The%enolase%peptides%will%be%low%or%
variable%but%the%PRTC%peptides%will%
be%fine
• If#something#happened#to#the#peptide#
cleanup#or#recovery
• Both%the%enolase%peptides%and%the%
PRTC%peptides%will%be%low%or%variable%

24. Each%Experiment%Gets%a%Folder
4

25. Each%Experiment%Gets%a%Folder
5

26. Each%Experiment%Gets%a%Folder
6

27. TaMADOR Page+Hosted+at+PanoramaWeb
https://panoramaweb.org/tamador.url

28. PanoramaWeb Examples/Beyond/TaMADOR
8
https://panoramaweb.org/tpad2.url https://panoramaweb.org/lincs.url

29. Backend(to(NIH(Branded(Sites
NCI$CPTAC$Assay$Portal LINCS$pilincs.org

30. Immutable)Data)Release)Via)Panorama)Public

31. Immutable)Data)Release)Via)Panorama)Public
1
Sharma(et(al.(MCP(2018

32. 32
Sharma(et(al.(MCP(2018

33. Linking&Results&with&Samples
3
• For$samples$in$the$sample$
manager
o Sample$linked$to$Skyline$docs$in$
Panorama$that$contain$results
• For$analyses$in$Panorama
o Results$linked$to$metadata,$
sample$locations,$etc…
• Groups,$labels,$etc…$added$to$
the$Skyline$document$
automatically

34. Vision:'
• Host%all%information%about%samples,%metadata,%preparation,%location,%etc..
• Use%that%information%to%design%experiments
• Track%system%suitability%and%process%controls
• Add%metadata%to%Skyline%from%Panorama.
• Batch%process%computationally%expensive%steps
• Manage%processed%data
o Audit%logs
o Version%control
• User%controlled%data%access
• Data%findable%upon%publication

35. Financial'Support
NIDDK'U01'(TaMADOR)
NIA'Nathan'Shock'Center
NIA'U19'and'P01
NIGMS'R24'Resource'Grant
NIGMS'BTRR'P41'Program
IARPA'Program
Hoofnagle'Lab
Andy'Hoofnagle'
Jess'Becker
Michelle'Emrick
North'Foulon
Elisha'Goonatilleke
Many'Others'
UW'Biochemistry
David'Baker'and'Lab
University'of'Washington
Department'of'Genome'Sciences
Bill'Noble
John'Stamatoyannopolous
Judit'Villen'and'Lab
Former&Lab&Members
Jarrett&&Egertson
Lindsay&Pino
Brian&Searle
Sandi&Spencer
Sonia&Ting
University'of'Washington
MacCoss'Lab
Nat&Brace
Rita&Chupalov
Brian&Connolly
Danielle&Faivre
Alex&Federation
Lilian&Heil
Eric&Huang
Rich&Johnson
Brendan&MacLean
Gennifer&Merrihew
Miranda&Mudge
Brook&Nunn
Deanna&Plubell
Brian&Pratt
Vagisha&Sharma
Nick&Shulman
Emma&TimminsJSchiffman
Kaipo Tamura
Christine&Wu
Stanford'
Tom'Montine'and'Lab
Kathleen'Poston
ThermoFisher
Jesse'Canterbury
Romain'Huguet
Claudia'Martins
Phil'Remes
Mike'Senko
Vlad'Zabrouskov
Acknowledgement
Software'Vendor'Support
Agilent Shimadzu
Bruker ThermoFisher
Sciex Waters
TaMADOR
Salvatore'Sechi'(NIDDK)
Andy'Hoofnagle'(UW)
Jenny'Van'Eyk (Cedars)
WeiXJun'Qian'(PNNL)
Jun'Qu'(University'of'Buffalo)
Kimia'Sobhani (Cedars)
Panorama'Partners