Table of Contents

guest
2018-12-10
Panorama: Repository Software for Targeted Mass Spectrometry Assays from Skyline
Panorama Partners Program
Documentation
   Create a folder in Panorama
   Folder navigation in Panorama
   Import data into Panorama
   Upload Raw Data
   Adding users to a project
   Submit Data to Panorama Public
   Quality control with AutoQC
   Install Panorama
Tutorials
   Tutorial: Sharing Skyline Documents
   Tutorial: Panorama Chromatogram Libraries
   Tutorial: Submitting Supplementary Data to Panorama Public
Webinars
   Panorama: An Introduction
   Panorama Targeted Proteomics Knowledge Base
   Panorama: Managing and Analyzing Large Datasets
   Panorama Public and Panorama AutoQC
   Introduction to Panorama 17.2
Publications
Dashboard
Example Data
Related
University of Washington

Panorama: Repository Software for Targeted Mass Spectrometry Assays from Skyline


Get started with Panorama today. Sign up to request a project on PanoramaWeb.Join the Panorama Partners Program to deploy your own Panorama server.
Browse the Panorama Public repository

Get Started


Panorama was developed with the following goals for targeted proteomics investigation:

  • Help labs aggregate curated results
  • Store the complete Skyline document data model
  • Use previous experiments to inform new experiments
  • Make it easy to search and review a large body of experiments
  • Facilitate sharing results
  • Keep private data secure

Panorama was designed to integrate with existing Skyline workflows.  Users can publish their documents to a Panorama server directly from Skyline.  Data on the server can be organized in folders, and users can take advantage of LabKey Server's fine-grained permission controls to securely share data with collaborators, or make it publicly available.  You can browse through some of the example experiments below to explore the Panorama UI for published Skyline documents. 

PanoramaWeb is a public Panorama server hosted at the University of Washington where laboratories and organizations can own free projects.  You can request a project on this server to find out what Panorama has to offer, without having to set up and maintain your own LabKey Server.  You will be able to explore all the available features in Panorama, and be given administrative rights to your project so that you can set up folders and configure permissions.  The LabKey Server security infrastructure will allow you to keep your data as private as you want or release it publicly when you are ready.

Panorama can also be installed by laboratories and organizations on their own servers.  Look at Install Panorama to get started. 

Events

Skyline User Group Meeting at ASMS 2018
Review the presentations

Skyline User Group Meeting at ASMS 2017
Review the presentations

Skyline User Group Meeting at ASMS 2016
Review the presentations

Recently Published

Panorama Public: A public repository for quantitative data sets processed in Skyline Vagisha Sharma, Josh Eckels, Birgit Schilling, Christina Ludwig, Jacob D. Jaffe, Michael J. MacCoss and Brendan MacLean. Molecular and Cellular Proteomics. 2018
[abstract]

An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments Michael S. Bereman, Joshua Beri, Vagisha Sharma, Cory Nathe, Josh Eckels, Brendan MacLean, Michael J. MacCoss. Journal of Proteome Research. 2016
[abstract] [pdf]

Managing Small Molecule Targeted Mass Spec Assays using Skyline and Panorama. Eckels J, Sharma V, Pratt B, Dunkley T, Wildsmith K, Anania V, Li Q, Nathe C, Patel B, MacCoss MJ, MacLean B. ASMS Poster. 2016
[pdf]

Performing quality control on targeted proteomics assays using Skyline and Panorama. Eckels J, Sharma V, Boss Y, Shi H, Dunkley T, Wildsmith K, Nathe C, Robinson A, Johnson R, Jaffe JD, MacCoss MJ, MacLean B. ASMS Poster. 2015
[pdf]

Panorama Public: A public repository for Skyline documents. Sharma V, Eckels J, Schilling B, Jaffe JD, MacCoss MJ, Brendan MacLean1 . ASMS Poster. 2015
[pdf]

Panorama: A Targeted Proteomics Knowledge Base. Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. Journal of Proteome Research. 2014
[abstract][pdf]

More Publications



Panorama Partners Program


Panorama is a freely-available, open-source repository server application for targeted proteomics assays that integrates into a Skyline proteomics workflow. It has been implemented as a module within LabKey Server, an open-source bioinformatics data management platform with extensive support for proteomics data and a security model rich enough to support clinical studies.

The Panorama Partners Program (P3) currently includes Roche (since 2013), Genentech (since 2013), Merck & Co., Inc. (since 2014), NCI-CPTAC (since 2017), and Amgen (since 2017) as members, as well as other multi-year pharma partners. It is designed to help organizations like these make the most of Panorama and its integration with Skyline, and provides a unique opportunity to help guide its development. It gives users a chance to engage directly with the Panorama and Skyline development teams, and help shape the direction of the projects to better suit the organization’s targeted mass spec needs.

Although P3 does not require that an organization have its own, in-house installation of LabKey Server and Panorama, it is very well suited to this approach. Unlike the free hosting provided on PanoramaWeb, an in-house installation helps satisfy strict organizational confidentiality requirements.

Membership in P3 is structured as a flat-rate annual subscription, and includes a professional edition subscription from LabKey. This provides full support and training for installation, maintenance, configuration, and general usage of LabKey Server, plus access to premium features. See the full list of items included.

Regularly scheduled conference calls give P3 members a chance to interact directly with both members of the MacCoss lab (the primary developers of Skyline and Panorama) and staff from LabKey (the primary developers of LabKey Server). MacCoss and LabKey staff will present updates on changes and improvements related to Panorama, and provide input on how to best use Skyline and Panorama to based on the organization’s needs. They will also solicit input on how Panorama might be improved or enhanced, and work to fit those changes into the upcoming development plans.

The program includes everything needed to adopt all of the existing Panorama functionality, and help ensure that the software continues to adapt to new requirements and workflows.

For more information, please contact LabKey.




Documentation





Create a folder in Panorama


To get your data into Panorama, first create a folder.

  • Hover over your project name in the menu bar below the Panorama icon and click on the New Subfolder icon shown in the image below. 

  • Select the Panorama option under Folder Type.  This is the folder type that should be selected for all workflows supported by Skyline (SRM-MS, MS1 filtering or MS2 based projects).  

 

  • On the Users / Permissions page select one of the available options and click Next.  You can also change permissions on a folder after it has been created.
  • The next page (Configure Panorama Folder) asks you to choose the type of Targeted MS folder you would like to create.  Panorama offers threechoices here.  
    • Choose the Experimental data option for folders that serve as a repository of Skyline documents, useful for collaborating, sharing and searching across multiple experiments. 
    • Choose Chromatogram library to store curated assays that can be used for designing and validating future experiments.  Check Rank peptides within proteins by peak area if your data contains relative peptide expression for proteins. 
    • Choose the QC option for tracking performance of mass spec. instruments over time. 

  • Click the Finish button. 

See the LabKey documentation for more information on creating and managing folders.




Folder navigation in Panorama


To navigate to your available projects and subfolders, hover over the folder icon or the current project name, located at the top left corner, just under the Panorama logo. 

Project navigation: Hovering over the folder icon to the left displays all the projects that you have access to on PanoramaWeb. Clicking on the project name (e.g. “MacCoss”) will take you to the home page of the project.

Folder navigation: The menu provides a tree view with expandible/collapsable nodes for navigation to sub-folders. Clicking on a folder name navigates to the home page of the folder.

Also see: LabKey Documentation: Navigate Server




Import data into Panorama


You can import data into a Panorama server either directly from Skyline or from Panorama's web-browser interface.

Importing data into a Panorama server from Skyline

Open the document that you want to publish to Panorama.

  • Click on the Upload to Panorama button in the toolbar, as shown below.  Alternatively, on the File menu, click Upload to Panorama.

  

  •  If you have not already registered a Panorama server in Skyline you will see the following message.

If you have an existing account on a Panorama server, and you would like to use that, click on Continue and enter the server details in the Edit Server form Skyline presents.  If you do not have an existing Panorama account, you can request a project on the PanoramaWeb server hosted at the University of Washington by clicking on Register.


In the Edit Server form enter the server URL and the email address and password for your account on the server. Click OK. Skyline will now display a form with the folder hierarchy on the Panorama server.

  • Select a folder on the server where you want to add the document.
  • Click the OK button. 

Skyline will create a ZIP archive of the files for your document and upload the ZIP file to the Panorama server, where it will be imported into the Panorama database. 

 




 

Importing data into a Panorama server via a web-browser

Using the Skyline Upload to Panorama toolbar button or menu item is the most convenient way to get your documents into Panorama.  But this can also be done by using the Panorama web interface.

  • In Skyline, open the file you want to import into Panorama.
  • In the File menu click Share.

  • Save the ZIP file on your computer using the Share Document form presented by Skyline.
  • In Panorama, navigate to your folder.
  • Click the Data Pipeline tab in the upper right corner.
  • Click on Process and Import Data as shown below.

  • In the Files browser, click Upload Files
  • Click the Browse button and select the file that you want to import.
  • Click the Upload button.

Once the file has been uploaded it will appear in the list of files in your folder

  • Check the box next to your file name.
  • Click Import Data in the toolbar, beside the Upload Files button

.

Wait for the file import to complete and then click the Panorama Dashboard tab in the upper right corner.  Your file should be listed under Targeted MS Runs. You can click on the file name to view the results. 

 






Upload Raw Data


Raw data associated with Skyline documents in a folder can be uploaded via the Raw Data tab in the top right corner.
(NOTE: If you don't see a Raw Data tab click here for instructions on how to add it)



Click the tab to see a Files browser. You can drag-and-drop files and/or folders located on your computer onto the Files browser as shown in the image below.



Another way to upload files is to click the Upload Files button in the Files browser, and click Browse to navigate to and select the file you want to upload.



Adding Raw Data Tab
The Raw Data tab is added by default when you create a new "Panorama" type folder. Some older folders may not have this tab. If you do not see the Raw Data in a "Panorama" type folder, and you are the administrator of the folder, you can add it as follows:
  • Click the gear icon in the top right corner
  • Select Add Raw Data Tab from the drop-down menu



More information on using the Files browser can be found here: Using the Files Repository



Adding users to a project


If you are the administrator of a project on panoramaweb.org, you can follow these steps to add users from your lab or organization to the project.

 

  • Click on the Gear Icon  , as shown in the image below.
  • Click Folder and then click  Permissions.

  • On the permissions page click on the Project Groups tab.
  • Click on the "Users" group.  This is a group that is created for every project on Panorama.

  • In the Users Information popup click on Manage Group.

  • Enter the email addresses of new users in the Add New Members text box. 
  • Click on Update Group Membership.

  • Any users that did not already have accounts on the Panorama server will be added to the system, and a welcoming email will be sent to them.
  • Click on Permissions in the navigation trail, as shown in the image below, to go back to the permissions page.

  • Assign the Users group to the Reader role, as shown in the image below.  All users that are members of the Users group will have read access to the project.

 

For more information on the adding / managing users and security roles look at the LabKey documentation on LabKey security architecture.




Submit Data to Panorama Public


PanoramaWeb hosts a public repository called Panorama Public where users may submit supplementary data associated with manuscripts that have been published or are under review. The repository provides a permanent location for data that can be referenced in publications. Users with data in their own projects on PanoramaWeb can follow the instructions below to submit the data to Panorama Public. The PanoramaWeb site administrators will review the submission request and make a copy of the data to Panorama Public. Reviewer account details will be provided to the submitter if the data is for a manuscript undergoing peer review, and the copy on Panorama Public will be kept private until the manuscript is accepted for publication. Data copied to Panorama Public is read-only, ensuring its availability in the original form accepted for publication.

New: Panorama Public is a now a member repository of the ProteomeXchange consortium. Data submitted to Panorama Public that fulfills ProteomeXchange submission requirements will be assigned a ProteomeXchange ID and announced on ProteomeCentral.

Submitting Data to Panorama Public

STEP 1: Upload Skyline documents to a folder on PanoramaWeb

Refer to the following wiki pages to create a folder in your project on PanoramaWeb and upload Skyline documents and associated data.


STEP 2: Prepare the folder for submission to Panorama Public

Folders containing supplementary data intended for submission to Panorama Public have to be annotated with a description of the experiment. This includes information such as an abstract, experiment and sample descriptions, organism, MS instruments used etc. To add experiment annotations to a folder, do the following:

  • Go to the home page of the folder by navigating the folder menu under the Panorama logo (Folder Navigation).
  • Click the gear icon in the top right corner of the page, then select Page Admin Mode from the drop-down menu.
  • Scroll to the bottom of the page and select Targeted MS Experiment from the <Select Web Part> menu at the bottom-left of the page.
  • Click the Add button. This action will add a web part titled Targeted MS Experiment at the bottom of the page that looks like this:
  • Click the Create New Experiment link in the Targeted MS Experiment web part.
  • Fill out the Targeted MS Experiment form.

The Instrument and Organism fields are auto-complete fields. Type 3 or more letters to see a drop-down list of matching options. Continue typing to refine the list and select from one of the available options. Contact the Panorama team if you do not see your instrument or organism in the list. At least one organism and one instrument is required for a ProteomeXchange submission.

In addition to an organism and an instrument, Keywords describing the data also need to be filled in for a ProteomeXchange submission. Contact details of the data submitter and a lab head are also required. In the Targeted MS Experiment form, the currently logged in user is auto-selected as the submitter. Please fill in the Submitter Affiliation for the submitting user. You can select a lab head from the drop-down menu in the Lab Head field which lists all users that have administrative privileges in the folder. If your lab head does not have an account on the server, you may create one by referring to Adding Users to a Project. If you do not wish to create an account for the lab head you can leave the Lab Head and Lab Head Affiliation fields blank. You will have the option of entering a lab head name and affiliation when you submit the data to Panorama Public.

  • Click the Submit button at the bottom of the form.
You will be taken to the experiment details page. All the Skyline documents that were uploaded to the folder where you added the Targeted MS Experiment webpart will get added to the experiment and will appear in the Targeted MS Runs table. If your data is organized in subfolders under the main folder, you should click the Include Subfolders button shown in the image below.


STEP 3: Submit the annotated folder to Panorama Public
  • Navigate back to the folder home page by clicking on the link with the icon and folder name near the top of the page.
  • Scroll down, if you need to, so that you can see the Targeted MS Experiment web part.
  • Click the red Submit button in the Targeted MS Experiment web part.


Your data will be checked for completeness for a ProteomeXchange submission. If there is missing information, such as missing raw data or missing metadata, it will be listed on a page after you click the Submit button. You can click the submit button again after you have provided all the missing information. Alternatively, if you do not want a ProteomeXchange ID for your submission you can proceed to the submission form by clicking the Continue without ProteomeXchange ID link shown below.


After you have provided all the missing information or clicked on the link to continue without a ProteomeXchange ID you will be presented with a form that looks similar to the one in the image below:


If you did not enter a lab head in the Targeted MS Experiment form, and a ProteomeXchange ID will be requested for your data, you will see additional fields in the form:

If you do not fill in the lab head details in this form, the submitting user's information will be used in the lab head field when announcing the data to ProteomeXchange.

In the Submission Request to Panorama Public form do the following:
  • Select “Panorama Public” from the drop-down list next to the Publish To option, if it is not already selected
  • Enter an Access Link
  • If you are submitting data for a manuscript undergoing peer review leave the Keep Private box checked. This will ensure that when the data is copied to Panorama Public, it will be kept private with read-only access to the submitter. Another read-only reviewer account will be created for the data, and account details provided to the submitter. The account details can be conveyed to the journal where the manuscript is submitted. If, however, you want your data to be publicly available on Panorama Public right away uncheck the Keep Private checkbox.
  • Click the Submit button
Access Link is the link that you will include in your manuscript to link to supplementary data on Panorama Public that can be viewed in a web browser. Initially, this link points to your folder on PanoramaWeb. But once a copy of your data has been made to Panorama Public, it will link to the location of the copied data on Panorama Public. This will be the permanent location of your supplementary data on Panorama Public.

The Publish Experiment form allows you to “build” these the access link. The initial part of the link remains constant: https://panoramaweb.org/. You can choose a string to complete the link (highlighted in yellow below).
https://panoramaweb.org/choose_a_string.url
The initial value entered in the Access Link field is a randomly generated alphanumeric string. You can replace it with a convenient, easy to remember string. This string has to be unique across all the experiments published to Panorama Public. You may get an error if the link you entered is already in use for another experiment on Panorama Public. If this happens change the text in the access link field and try again.

Requests to copy data are handled by Panorama Public administrators within a week of submission. Once your data has been successfully copied to Panorama Public you will receive a confirmation email. If you requested that your data on Panorama Public be kept private (e.g. for a manuscript under peer review), the confirmation email will also include reviewer account details. You can pass on the account details to the journal where you are submitting your manuscript. The confirmation email will also include a ProteomeXchange ID unless you opted to skip ProteomeXchange submission.

Once the form is submitted successfully you can go back to the experiment details page.

In the Experiment Details box, just above the experiment title, you will see a “Copy Pending!” message. This message will disappear once your data has been copied to Panorama Public. Any changes that you make in the folder, such as adding/removing Skyline documents or wiki pages, or changing the layout of the page will also get copied when a copy is made to Panorama Public. At the bottom of the page, in the Submission table, you will see the Access Link that you created for this experiment. The Copied column will be blank until a copy has been made successfully. Once the data has been copied this column will display the date when the data was copied. And at that point if you click the Access Link you will be taken to the location on Panorama Public where your data was copied. You can verify that the data, folder layout and views were copied accurately.


If you need to make any changes to your data (e.g. to address reviewer feedback) after it has been copied to Panorama Public you can make the changes in your own folder. When you are ready click the red Resubmit button in the Targeted MS Experiment web part. This will send a request to the Panorama Public administrators to delete the old copy and make a new copy of your data to Panorama Public. Your access link will remain unchanged.


Related Resources:



Quality control with AutoQC


Skyline and Panorama combine to provide a robust QC workflow for LCMS instrumentation used in proteomics experiments. AutoQC Loader, a utility application, uses SkylineRunner to invoke Skyline without user interface for automated data processing. AutoQC Loader can be run on an instrument control computer to capture new QC runs automatically, and add them to an existing Skyline document, where the information is archived for later use and transferred to Panorama. Panorama retains a full history of QC run performance, and presents users with interactive plots for key metrics including retention time and peak area. Additionally, users can add information about changes including instrumentation, maintenance, and reagents, which are overlaid on the plots, providing a convenient way to correlate cause and effect.

[Install] AutoQC Loader for Skyline 3.5 or later
Note:You can download and install AutoQC Loader unplugged on computers with issues connecting directly to the internet.

[Install] AutoQC Loader-daily for Skyline-daily (3.1.1.8694 or later)
Note:You can download and install AutoQC Loader-daily unplugged on computers with issues connecting directly to the internet





Install Panorama


Panorama has been implemented as a module within LabKey Server, and is included in the official release of LabKey Server as of v12.3.  You can download the latest release of LabKey Server here for a new installation or to upgrade an existing one.  See LabKey installation documentation for available install options.

Once you have a running LabKey Server you can set up a workspace for your lab or group by creating projects and folder, and configuring user and group permissions for authenticated access to the workspace.  Please see the LabKey documentation for:

For additional documentation and help regarding Labkey Server please visit the LabKey support page.

For information on creating folders in Panorama, see Create a folder in Panorma

For more information on getting your data into a Panorama server see Import data into Panorama.




Tutorials


Try one of these tutorials, and get hands-on experience using Panorama with real data.

Sharing Skyline Documents 

Panorama Chromatogram Libraries 

Publish to Panorama Public 

On Oct 20, 2015, the Skyline and Panorama Teams produced Webinar #11: Panorama Public and Panorama AutoQC, another great resource to learn more about some of the new aspects of Panorama.
[webinar]




Tutorial: Sharing Skyline Documents



Overview

Panorama is a freely available, open-source web server database application for targeted proteomics assays that integrates into a Skyline proteomics workflow. It has been implemented as a module within LabKey Server, an open-source bioinformatics data management platform with extensive support for proteomics data and a security model rich enough to support clinical studies.

Panorama can be installed by laboratories and organizations on their own servers. You can visit the LabKey Server installation documentation: https://www.labkey.org/wiki/home/Documentation/page.view?name=installServerDemo for the available installation options. For this tutorial you will use the Panorama server hosted at the University of Washington panoramaweb.org where users can request free projects and have full administrative rights to configure data organization and security. This tutorial is an introduction to Panorama and covers the following areas:

  • Requesting a project on panoramaweb.org
  • Data organization and folder management in Panorama
  • Publishing Skyline documents to Panorama
  • Data display options and searching results uploaded to Panorama
  • Providing access to collaborators and other groups

Getting Started

  • To start this tutorial, download the following ZIP file:
  • Extract the files in it to a folder on your computer, such as
    C:\Users\userName\Documents
  • This will create a new folder:
    C:\Users\userName\Documents\PanoramaSharing
It will contain all the files necessary for this tutorial.

Requesting a Project on panoramaweb.org

Open the Study9S_Site52_v3.sky file in Skyline either by double-clicking on the file in Windows Explorer or by going through the File > Open menu in Skyline. This file contains results that are part of a recent CPTAC multi-site SRM-MS system suitability study (Abbatiello et al., Mol. Cell. Proteomics 2013). The data in this document was collected at Site 52. To publish this document to Panorama, click on the Publish to Panorama button in the toolbar, as circled below. Alternatively, on the File menu, click Publish to Panorama.

Since you have not yet registered a Panorama server in Skyline, you will see the following message:

  • If you have an existing account on a Panorama server, and you would like to use that, click Continue and enter the server details in the Edit Server form Skyline presents.
  • If you do not have an existing Panorama account, click Register to request a project on the PanoramaWeb server hosted at the University of Washington. This will open the project sign-up page on panoramaweb.org in a web-browser as shown below.
  • Fill out the form and be sure to enter a Group name.
  • Click Submit
The group name is used to create projects on panoramaweb.org. The Panorama team reviews all project requests and, upon approval, creates a project with the requested group name. If you are looking for a space to work through this tutorial and explore Panorama, please enter "Tutorials" in the Group name, and a folder with full administrative rights will be created for you in the Tutorials project on panoramaweb.org. Otherwise, enter your preferred project name. Once your project or folder has been created, you will receive a welcoming email with a link to setup a password for your account. After you have completed the registration process you can sign-in to panoramaweb.org. On the home page, click the Projects tab to see a list of all the projects to which you have access on panoramaweb.org. If you entered "Tutorials" in the project sign-up form, you will see the Tutorials project where a folder was just created for you.

Click on the Tutorials project to go to the project homepage. On the project homepage, hover over the project name in the menu bar below the Panorama icon, click the to open the Tutorials node, then click on the folder that was created for you (e.g. ‘Your_Username’ in the following screenshot). You will have full administrative rights in your folder, so you will be able to create a folder structure for organizing your Skyline documents, and configure user access to the sub-folders.

Creating a Subfolder in Panorama

Skyline documents cannot be uploaded to the root project folder on panoramaweb.org or your folder in the ‘Tutorials’ project. You will create a sub-folder for uploading the Skyline document that you opened earlier. As a project administrator, you would typically organize your project workspace to have subfolders for each project and/or each researcher in your laboratory or organization. Follow these steps to create a "system suitability" sub-folder in your folder in the “Tutorials” project:

  • Navigate to "Your_Username" folder home page, if you are not already there.
  • Hover over the project name in the menu bar below the Panorama icon and click on the new folder icon shown in the image below.
  • In the Create Folder form, enter "system suitability" in the folder Name field.
  • Select the Panorama option under Folder Type. This is the folder type that should be selected for all workflows supported by Skyline (SRM-MS, MS1 filtering or MS2 based projects).
  • Click Next.
  • On the "Users / Permissions" page accept the default selection and click Next. You will configure user permissions on this folder later.
  • The next page Configure Panorama Folder asks you to choose the type of Targeted MS folder you would like to create. Panorama offers three choices here. For this tutorial accept the default Experimental data option. This option is meant for folders that serve as a repository of Skyline documents, useful for collaborating, sharing and searching across multiple experiments.
  • Click Finish.

You will be taken to the home page of the "system suitability" sub-folder that should look as follows:

You are now ready to upload Skyline documents to this folder.

Publishing Data from Skyline to Panorama

To publish your first Skyline document to PanoramaWeb, perform the following steps:

  • Open "Study9S_Site52_v3.sky" in Skyline if it is not already open.
  • If the Edit Server form is not already open, open it by clicking the Publish to Panorama button, or selecting File > Publish to Panorama and clicking Continue in the popup.
  • In the Edit Server form, enter the email address and password with which you registered on panoramaweb.org. The server URL should already be entered as https://panoramaweb.org.
  • Click OK.
Skyline will now display a form with the folder hierarchy on panoramaweb.org. Only the folders to which you have access will be displayed.
  • Navigate to and select the "system suitability" folder.
  • Click OK.

Skyline will create a ZIP archive of the files for your document and upload the ZIP file to panoramaweb.org, where it will be imported into the Panorama database.

A popup message reading "Publish succeeded, would you like to view the file in Panorama?" will appear. Click Yes to view the document details.

Viewing Data in Panorama

If you are not already viewing the document details, return to your "system suitability" folder, refresh the browser window if necessary, and click the name of the file you just uploaded in the Targeted MS Runs box.

The Document Summary box shown in image below gives you a summary of the number of proteins, peptides, and transitions in your document.

Below the Document Summary box you can view a list of all the proteins, peptides and precursors in your document, along with some of the information imported from the Skyline document, such as a modified peptide sequence, m/z and charge. You can click on a protein or peptide to view more details, including chromatograms and some of the other graphs that are also available in Skyline. Scroll down on the page and click on the peptide CAVVDVPFGGAK. This will take you to a page that has the following details for this peptide:

1. Chromatograms to show quantitative data quality

This peptide was measured in 10 QC system suitability replicates and there were 3 blank acquisitions. On this page you can view the chromatograms for this peptide in all the replicates. The image below shows the precursor and transition chromatograms in the replicates QC_01 and QC_02. There is one row of chromatograms for each replicate in your Skyline document, where the first column has the total precursor chromatogram and the subsequent columns have transition chromatograms. If this precursor was measured in a light as well as a heavy-labeled from, transition chromatograms for both the forms would be displayed side-by-side.

2. Peak Area Replicate Graph

Scroll further down on the page or collapse the Chromatograms box by clicking on the icon in the header of the box as circled in the image above.

In the Summary Charts panel, you will now see a graph displaying the peak area for this peptide in the 13 replicates. This graph is similar to what you would see in Skyline for this peptide.

As in Skyline, Panorama also allows grouping peak areas by custom replicate annotations. In this Skyline document researchers used a custom "system suitability" annotation that was set to "true" for the system suitability replicates and "false" for the blank acquisitions. You can group the peak areas by selecting "system suitability" from the pull-down combo-box next to Group By.

Click Update to see peak areas grouped by the "system suitability" annotation.

In the graph above, the red bar labeled ‘true’ represents the 10 system suitability runs, and the small error bar indicates that there was very little variability in the measurements for this peptide in the 10 replicates. You can also switch to a Coefficient of Variation (CV) view by checking the CV Values box and clicking Update again.

3. Library MS/MS spectrum viewer

Scroll down further on the peptide details page to see an interactive spectrum viewer displaying the MS/MS spectrum for CAVVDVPFGGAK from the spectrum library associated with this Skyline document. The name of the library is displayed in the title bar of the viewer. The viewer allows you to zoom in by clicking and dragging your mouse over the spectrum. You can also customize the view by selecting the ion types and charge states you want to display from the options menu to the left of the spectrum. A color-coded table to the right of the spectrum lists all the fragment ion m/z values for the peptide, with colored boxed representing the matching fragment ions found in the library spectrum. These spectral library views can be used to support publications in peer-reviewed journals or share data with collaborators.

Customizing Grid Views in Panorama

On your web-browser click the back button, or scroll to the top of the page and click on the ZIP file name in the navigation trail just under your folder name as shown in the image below. This will take you back to the documents details page.

LabKey Server, on top of which Panorama is built, allows customizations of all tabular views. You can select which columns you would like to see, order them according to your preference, and define a sorting order. The Precursor List table on this page has blank annotation columns since the researchers did not define any custom peptide or precursor annotations in this Skyline document.

To hide these columns from the default view preform the following steps:

  • Select (Grid Views) just under the Precursor List heading.
  • Choose Customize Grid from the drop-down menu.

In the customization form that appears, you will see the Selected Fields panel on the right that shows the fields that are currently displayed.

  • Hover over "Peptide Note/Annotations" below Peptide in the Selected Fields and click the (remove) icon.
  • Do the same for "Precursor Note/Annotations" below Precursor.
  • Click Save.
  • In the popup, leave "Default grid view for this page" checked.
  • Check "Make this grid view available to all users". This will cause all users with access to this folder to see the same table columns.
  • Click Save.

The annotation columns should no longer be displayed, as shown below:

You can view the LabKey Server documentation on customizing grid views (https://www.labkey.org/wiki/home/Documentation/page.view?name=customViews) for more information.

Downloading Skyline Files from Panorama

Scroll up, if you need to, to view the Document Summary box. You can download the original Skyline ZIP archive that was published to Panorama by clicking on the Download link next to the file name.

To open this zip file in Skyline do the following:

  • On the File menu, click Open (Ctrl-O).
  • Navigate to and select the zip file that you downloaded.
  • Click the Open button.

Publishing to Panorama provides a convenient way to share Skyline documents with other researchers. You will see later in this tutorial how to give other users access to the folders you create in Panorama.

Uploading Documents Using the Panorama Web Interface

Using the Skyline Publish to Panorama toolbar button or menu item is the most convenient way to get your documents into Panorama. But this can also be done by using the Panorama web interface. Next, you will use the web-interface to upload another document to the "system suitability" folder.

  • In Skyline, open the file "Study9S_Site54_v2.sky".
This file contains results acquired at another site in the CPTAC system suitability study. Prepare this file for upload to Panorama by doing the following:
  • In the File menu, click Share.
  • Click the Minimal button in the form that appears.
  • Save the ZIP file on your computer using the Share Document form presented by Skyline.
  • In Panorama, go to the "system suitability" folder.
  • Click the Data Pipeline tab in the upper right corner.
  • Click Process and Import Data as shown below.
  • In the Files browser, click Upload Files.
  • Click Browse or Choose File.
  • Select "Study9S_Site54_v2.zip" that you just saved through Skyline.
  • In the Description field enter "Site 54".
  • Click Upload.

Once the file has been uploaded it will appear in the list of files in your folder.

  • Check the box next to Study9S_Site54_v2.zip.
  • Click Import Data in the toolbar.
  • Confirm that Import Skyline Results is selected.
  • Click Import in the Import Data popup.
Wait for the file import to complete and then click the Panorama Dashboard tab. You will now see 2 files (from sites 52 and 54) available under Targeted MS Runs.

Search Features in Panorama

Panorama allows you to search for proteins, peptides and even peptides with specific modifications across all the documents contained in a folder and its sub-folders. These search features are particularly useful for large projects and data sets, and help to compare results between data acquired over a long period of time.

On the "system suitability" folder page look at the Mass Spec Search box. You will see three available search options under the tabs Protein Search, Peptide Search and Modification Search. You will use the modification search option later in the tutorial. To perform a peptide search do the following:

  • Click the Peptide Search tab.
  • Enter "GFCGLSQPK" in the Peptide sequence field.
  • Check Exact matches only.
  • Click the Search button.

On the results page, in the Targeted MS Peptides box, you will see a list of documents in your folder where this peptide was observed. This peptide was found in both documents uploaded (sites 52 and 54) to this folder. You can view the details for the peptide in a document by clicking on the peptide sequence.

Sharing Data in Panorama

Panorama allows you to set fine-grained access control on your folders. You can grant access to your folders to individual collaborators or groups of researchers, and you can also configure the type of access (read-only, read and edit etc.).

To change the permissions on the "system suitability" folder, first, make sure that you are on the "system suitability" folder page. If not, return by hovering over your project name (e.g. Tutorials) in the menu bar below the Panorama icon, opening the project and folders, then clicking your "system suitability" folder as shown in the image below.

To change the permissions on this folder, navigate to the Permissions page by doing the following:

  • On the menu bar, choose (Admin) > Folder > Permissions.

If you did not configure the permissions for this folder during the folder creation process, the permissions page should look like this.

The email address selected for the Folder Administrator role should be the email address with which you requested a project on panoramaweb.org. The Folder Administrator has full control over a folder. To add Brendan MacLean (Skyline team) to the Editor role, which will give him the ability to add and delete documents to this folder, follow these steps:

  • Uncheck "Inherit permissions from parent", if it is checked.
  • Select ‘brendanx@uw.edu (Brendan MacLean)’ from the combo-box next to Editor.
  • Click Save.
To add Vagisha Sharma (Panorama team) to the Reader role:
  • Select ‘vsharma@uw.edu’ from the combo-box next to Reader.
  • Click Save.
The Reader role allows users to view data in a folder but they may not add or delete documents. The permissions page should now look like this:

Instead of adding individual users to a role you can create a group of users and assign a role to the group. Only Project Administrators have permissions to create user groups. If you are working in your folder in the “Tutorials” project on panoramaweb.org, you do not have project administrator privileges. However, if you are working through this tutorial in your own project on panoramaweb.org or any other Panorama server, follow these steps to create a "Seattle collaborators" group and assign it to the Reader role:

  • On the Permissions page click on the Project Groups tab.
  • In the New group name field enter "Seattle collaborators" and click Create New Group.
  • In the popup select Brendan and Vagisha from the pull down list to add them to the group.
  • Click Done.
  • Select the Permissions tab.
  • Add the new "Seattle collaborator" group to the Reader role.
  • Click Save.
  • Select your "system suitability" folder in the folder navigation column.
  • Add the "Seattle collaborator" group to the Reader role for this folder.
  • Click Save and Finish.
Members of the "Seattle collaborators" group will be able to view the "system suitability" folder if they have a direct link to the folder. They will not be able to view the parent folder (e.g. Your_Username) on the home page or navigate to the "system suitability" folder through the folder navigation UI. To access a folder from the UI, users or user groups require read permissions not only on the folder but also on the parent folders all the way up to the root project folder. To enable the "Seattle collaborators" group to access the "system suitability" folder via the navigation UI, assign the Reader role to this group in the parent folder (e.g. Your_Username).

You can add more users later to the "Seattle collaborators" group. All users in this group will have read access to the "system suitability" folder. If you would like to add a user to the "Seattle collaborators" group that does not already have an account on Panorama, you can do that by following these steps:

  • Select (Admin) > Folder > Permissions.
  • Click the Project Groups tab.
  • Click the "Seattle collaborators" group.
  • In the popup, click Manage Group.
  • On the Manage Group page, enter the email address of the new user in the Add New Members field.
  • Scroll down and click Update Group Membership.
An email will be sent to the new user and they will be able login to view the data in the "System suitability" folder once they setup a password for their account.

You can view the LabKey Server documentation on configuring permissions (https://www.labkey.org/wiki/home/Documentation/page.view?name=configuringPerms) for more information.

Viewing of PTM-containing Peptides in Panorama

Many journals require visual display of MS/MS spectra of peptides containing post-translational modifications such as phosphorylation or acetylation. You can make use of Skyline to build spectral libraries from your peptide search results and view the annotated spectra in the Skyline Spectral Library Explorer. However, using the resulting Skyline document to satisfy journal requirements requires that you send the Skyline document to reviewers, and that they have a local installation of Skyline to view the document. Alternatively, you can publish the documents to Panorama, where reviewers can view the spectra in the Panorama spectrum viewer.

Next, you will import a Skyline document to Panorama that contains phosphorylated peptides, search for modified peptides and view their spectra.

Create a new sub-folder in "Your_Username" folder called "Phospho peptides", using another method for creating sub-folders in Panorama than you used before:

  • In the header bar, select (Admin) > Folder > Management.
  • On the Folder Management page, make sure that the Folder Tree tab is selected, and "Your_Username" folder is highlighted.
  • Click Create Subfolder.
  • In the Create Folder wizard enter Name: “Phospho peptides”.
  • Select Folder Type, "Panorama" as before.
  • Click Next.
  • For Users/Permissions keep the default selection: Inherit from Parent Folder.
  • Click Next.
  • Select Experimental Data on the Configure Panorama Folder page.
  • Click Finish.
To add to the new folder a Skyline document containing a spectral library from a phosphorylation experiment, perform the following steps:
  • In Skyline, open the file "Phospho_0921_2010_Thr99_v1_P only.sky" from the tutorial folder.
  • Click the Publish to Panorama toolbar button.
  • Select the “Phospho peptides” folder from the folder tree in the Publish Document dialog.
  • Click OK.

Wait for data import to complete and then go back to Panorama in your web-browser, and navigate to the “Phospho peptides” folder. Refresh the page (F5 in most browsers) if you are already on the “Phospho peptides” folder page. You should see the file that you just imported to Panorama in the Targeted MS Runs table. Click on the name of the file to see the document details. Clicking on any of the peptide sequences will take you to the peptide details page where you can view the library spectrum for the peptide. Click the back button to go back to the folder page, or use the Phospho peptides link.

To find all peptides in this document containing a phosphorylation, perform the following steps:

  • In the Mass Spec Search box, select the Modification Search tab.
  • Choose the Delta Mass option for Search By, if it is not already selected.
  • Enter "S" in the Amino Acid field.
  • Enter "80" in the Delta Mass field.
  • Click Search.

You will now see a list of all the serine phosphorylated peptides in the document. Click on the first peptide in the list, LSVPTSDEEDEVPAPKPR, to view its library spectrum. Click back in your browser. In the Peptide Summary box click on the name of the protein (sp|Q8NE71|ABCF1_HUMAN) to which this peptide belongs.

You will be taken to the protein details page where you can see the location of this peptide in the protein sequence.

Conclusion

In this tutorial, you have been introduced to new ways you can share Skyline documents with collaborators, reviewers and the general public using Panorama, and the PanoramaWeb.org web site hosted by the MacCoss Lab at the University of Washington. You have requested a project on PanoramaWeb, registered an administrator account for that project with your email address, and created 2 new folders in that project. You have explored data from Skyline documents in these folders, searched for specific peptides and post-translational modifications, and customized access to the data in them. If you worked on this tutorial in your own project instead of the "Tutorials" project, you can now just as easily go back to the folder management form and delete these tutorial folders to return your new project to its original state, ready for your own experimental data.

We wish you luck in your research and hope that you find these tools useful in sharing and disseminating your findings.




Tutorial: Panorama Chromatogram Libraries



Overview

Targeted assay development for proteins or peptides is typically a time-consuming and lengthy process. Deciding the ideal set of peptides and transitions to measure for your proteins of interest requires careful experimental design and iterative optimization. Once an assay has been established, the assay parameters can be reused for designing future experiments. Chromatogram libraries in Panorama provide a way you can store targeted assays that have been curated in Skyline and reuse them in the future for measuring proteins and peptides in other samples, as well as share them with other researchers. Chromatogram libraries can also capture physiochemical and experimental properties such as the relative ion abundance, measured retention time, measured chromatograms, and in the future we expect to store iRT, ion mobility, and optimal instrument parameters such as collision energy. Empirical measurements for these parameters can be particularly relevant in guiding targeted experiment design.

In this tutorial we will:

  • Create a folder in Panorama for chromatogram library data.
  • Add Skyline documents, with curated targeted results, to the chromatogram library folder.
  • Download the chromatogram library from Panorama and use it in Skyline.

Getting Started

To start this tutorial, download the following ZIP file:

Extract the files to a folder on your computer, like:
C:\Users\username\Documents

This will create a new folder:

C:\Users\username\Documents\PanoramaChromatogramLibraries

It will contain all the files necessary for this tutorial.

The data used in this tutorial was published in Stergachis et al. 2011, where the authors described a high-throughput method for selecting optimal peptides and fragment ions for targeted proteomics applications. The Skyline files used in this tutorial contain assays for a subset of the 96 human transcription factors on which they demonstrated their approach.

Signing Up for an Account on panoramaweb.org

This tutorial assumes that you will be working in a sub-folder of the "Tutorials" project on panoramaweb.org, the Panorama server hosted by the MacCoss lab at the University of Washington. However, if you already have an existing account and project on panoramaweb.org, or have an account on another Panorama server you are welcome to use that, and skip to the next step.

To request a folder on panoramaweb.org for working through this tutorial, fill out the sign-up form on this page: https://panoramaweb.org/labkey/wiki/home/support/page.view?name=hosted-project-signup-form

  • Fill in the required fields, marked with a red asterisk, in the form shown below.
  • Enter "Tutorials" in the Group name.
  • Click Submit.

Once your request is approved, a folder with full administrative rights will be created for you in the "Tutorials" project on panoramaweb.org. You will receive a welcoming email with a link to complete your account registration by choosing a password.

Creating a Chromatogram Library Folder in Panorama

First sign in to the Panorama server and navigate to your folder. If you are working in the "Tutorials" project on panoramaweb.org follow these steps:

  • Click the Projects tab to see a list of all the projects to which you have access on the server.
  • Click the "Tutorials" project.
  • On the project homepage, hover over the project name in the menu bar below the Panorama icon and click on the folder that was created for you (e.g. "Your_Username").

When organizing your data for chromatogram libraries, we recommend that you create a folder for each species that you study, and under each species folder you can create subfolders for the instrument type where the data was collected, or any other experimental conditions for which it is appropriate to have separate chromatogram libraries. In this tutorial you will create a subfolder for building a chromatogram library for human transcription factors. To create a sub-folder for this tutorial, do the following:

  • Hover over the project menu and click the new folder icon shown in the image below.
  • In the Create Folder form, enter "Human" in the folder Name field.
  • Select the Panorama option under Folder Type, as shown below.
  • Click Next.
  • On the Users / Permissions page accept the default selection.
  • Click Next.
  • On the Configure Panorama Folder page choose the Chromatogram library option.
  • Check the box to "Rank peptides within proteins by peak area".
  • Click Finish.
The Rank peptides within proteins by peak area box should be checked when you have targeted results containing relative peptide peak areas for a given protein. Leave this box unchecked if you do not yet have quantitative data from proteolytically digested proteins, such as when you are working with synthetic peptides.

After successful folder creation, you will be taken to the home page of the "Human" chromatogram library folder that should look as follows:

You are now ready to upload Skyline documents to this folder.

Publishing Skyline Documents to a Library Folder in Panorama

Open the "Stergachis-SupplementaryData_2_a.sky" file in Skyline either by double-clicking on the file in Windows Explorer or in Skyline, on the File menu, click Open (Ctrl-O). This file contains peptides and fragment ions for 10 human transcription factors published in Stergachis et al. 2011. To publish this document to your library folder on Panorama, follow these steps:

  • Click on the Publish to Panorama button in the Skyline toolbar, shown in the image below. Alternatively, on the File menu, click Publish to Panorama.

If you have not yet set up a Panorama server in Skyline, you will see the following message.

  • Click Continue.
In the Edit Server form that appears, the default value in the URL field is https://panoramaweb.org. This is the URL of the server hosted at the University of Washington, and the server where you have an account if you followed the registration steps at the beginning of this tutorial.
    • If you are working on a server other than panoramaweb.org, enter the URL of your server.
    • Enter your email address and password on the Panorama server.
    • Click the OK button.
Skyline will now display a form with the folders available to you on your Panorama server. Chromatogram library folders will have the chromatogram icon next to them.

  • Navigate to and select the "Human" folder that you just created in Panorama.
  • Click the OK button.
Skyline will upload a ZIP archive of your document to the selected library folder on the Panorama server.

Viewing Chromatogram Library Data in Panorama

Once your document has been imported into Panorama, go back to the web-browser where the home page of the "Human" library folder should still be open. Skyline will offer you the option to directly view the results. From this page click Human to return to the home page. Refresh the page (F5 in most browsers) and, in the Chromatogram Library Download box, you will see that the first version (Revision 1) of your "Human Library" is now available for download. A brief summary of the contents of the library is also displayed under the Library Statistics heading.

Further down on the page, in the Mass Spec Search box, you can search for proteins, peptide sequences or peptides with specific modifications in your library.

The tables below the Mass Spec Search box display a list of the proteins and peptides in the library folder. Clicking on an entry in one of these tables will display more details for the selected protein or peptide. Click on CTCF in the Proteins table to bring up a page with more details for this protein. The Sequence Coverage box displays the sequence, with colored rectangles highlighting the peptides for which there are measurements in the library.

The Peptides table displays a list of these peptides along with some information that was contained in the uploaded Skyline document, such as the retention time.

Below the Peptides table is a bar graph that displays the peak areas of the peptides, ordered from the highest to the lowest measured peak area. Retention times are also shown.

Go back to the home page of your library folder either by clicking your browser's back button or by clicking the Human (folder name) link near the top of the page.

Updating Chromatogram Libraries

As you develop assays for more proteins or peptides, you can publish Skyline documents containing those assays to the same library folder. Panorama will build a new version of the library each time a Skyline document is published to the folder. Any proteins that were not already included in the library will be added.

Open the file "Stergachis-SupplementaryData_2_b.sky" in Skyline. This file contains another subset of transcription factor assays from "Stergachis et al. 2011|#reference]. This file also contains measurements for the transcription factor MAX that was already included in the first document that you published to the library folder. Two additional peptide measurements are included for this protein in this document.

Publish this document to the "Human" chromatogram library folder on Panorama by doing the following:

  • Click the Publish to Panorama button in the Skyline toolbar.
  • Select the "Human" folder in the Panorama Folders tree of the Publish Document form.
  • Click OK.
  • Wait for the file import to complete.
  • Go to your browser and refresh the library folder page on PanoramaWeb. If you click Yes in Skyline to "view the file in Panorama", you will open a new browser showing the results. Click Human near the top of the page to return to the library folder page.
You will see that a new version of the library is now available in Panorama, as indicated by the higher revision number (2) in the Chromatogram Library Download box. This library includes the new proteins, peptides and transitions from the Skyline file that you just uploaded, reflected in the updated library statistics. You should also see a warning message below the library statistics about a conflicting protein. This message is displayed because the document you just uploaded contains a protein (transcription factor MAX) which already existed in the library.

In case of a conflict, Panorama marks the incoming version of the protein as conflicted, and continues to include the older version of the protein in the library, until the conflict is resolved. The library built after uploading "Stergachis-SupplementaryData_2_b.sky" still contains peptides, transitions and chromatograms for protein MAX from the first document that was uploaded to the library folder. To tell Panorama to use the newer version of the protein:

  • Click the Resolve conflicts link.
You will now see a table containing a list of conflicting proteins displayed side by side. The left column, titled Conflicting Proteins in Document, displays the version of the protein contained in the document that you just uploaded. The right column, titled Current Library Proteins has the version contained in the current library.

Click on the (plus) icon next to the protein name to view the list of peptides measured for this protein in the two versions. (When expanded, the icon will become a (minus). The new document contains measurements for two additional peptides that are marked in the image below.

To resolve this conflict by choosing the new version of the protein, do the following:

  • Under Conflicting Proteins in Document, click the check box next to the protein name if it is not already checked.
  • Click Apply Changes.
Panorama will now rebuild the library and include the new version of the protein with all its peptides and transitions. Any peptides or transitions that existed only in the older version of the protein will be removed from the library. Once the new library has been built you will be taken to the home page of the library folder where you will see that a new revision (3) of the library is available. The conflict message should no longer be displayed.
  • Click on the Download button and save the chromatogram library file (Human_rev3.clib) to your computer.
You will use this library in the next section of the tutorial.

You can access older revisions of the library by clicking on the Archived Revisions link below the library file name, shown in the image below.

A table with all the library revisions will be displayed. You can download older revisions by clicking on a file name in the Archived Revisions table.

Using Chromatogram Libraries in Skyline

You will now prepare a new Skyline document to measure the proteins CTCF and MAX in another sample. The library you just downloaded from Panorama contains chromatograms for peptides from these proteins. You will use the library to filter the set of peptides and transitions in your Skyline document to the best responding ones contained in the library. You will also see how you can compare fragment ion or transition chromatograms obtained in a new experiment with chromatograms contained in the library to confirm peptide identifications.

Before you begin, make sure that the peptide and transition settings in Skyline are configured correctly, by creating a new file and adjusting its settings as necessary:

  • On the File menu in Skyline, click New (Ctrl-N).
Configure the peptide settings as follows:
  • On the Settings menu, click Peptide Settings....
  • Click the Digestion tab, if it is not already selected.
    • In the Enzyme dropdown list, select "Trypsin KR " (if it is not selected by default).
    • In the Max Missed Cleavages dropdown list, select "0" (if it is not selected by default).
    • In the Background proteome dropdown list, select "None" (if it is not already selected).
  • Click the Filter tab.
    • In the Min length field, enter "7".
    • In the Max length field, enter "23".
    • In the Exclude N-terminal AAs field, enter "0".
    • Uncheck Exclude potential ragged ends (if it is checked).
    • Uncheck any selected options in the Exclude peptides containing: list.
    • Check Auto-select all matching peptides (if it is not already checked).
  • Click the Library tab.
    • Uncheck any selected libraries.
  • Click on the Modifications tab.
    • Check the "Carbamidomethyl (C)" modification in the Structural modifications list (if it is not already checked).
    • Uncheck any other selected modifications in the Structural modifications list.
    • Uncheck any selected modifications in the Isotope modifications list.
  • Click the OK button in the Peptide Settings form.
Configure the transition settings as follows:
  • On the Settings menu, click Transition Settings....
  • Click the Filter tab.
    • In the Precursor charges field, enter "2".
    • In the Ion charges field, enter "1".
    • In the Ion types field, enter "y".
    • In the Product ions section From dropdown list, select "ion 3".
    • In the Product ions section To dropdown list, select "last ion – 1".
    • In the Special ions list, uncheck any selected options.
    • Make sure that the Precursor m/z exclusion window field is blank.
    • Check Auto-select all matching transitions (if it is not already checked).
  • Click on the Library tab.
    • Uncheck If a library spectrum is available, pick its most intense ions.
  • Click on the Instrument tab.
    • Enter "50" in the Min m/z textbox.
    • Enter "1500" in the Max m/z textbox.
    • Uncheck Dynamic min product m/z if it is checked.
  • Click the OK button in the Transition Settings form.
The files you downloaded for this tutorial include the file "CTCF_MAX.txt". This file contains sequences for the proteins CTCF and MAX. To add these proteins to the new Skyline document do the following:
  • On the File menu, choose Import and click FASTA....
  • Browse to and select "CTCF_MAX.txt" in the file browser.
  • Click the Open button.
The Skyline window should now look like this:

The settings you configured in Skyline have resulted in 31 peptides for the two proteins. If you export a transition list for this document without applying any filtering you would be measuring 220 transitions. However, you can take advantage of the information contained in the chromatogram library to limit your measurements to the best responding precursors and product ions for the two proteins. Follow these steps to filter the list of peptides and transitions:

  • On the Settings menu, click Peptide Settings....
  • Click the Library tab.
  • Click the Edit List button.
  • Click the Add... button in the Edit Libraries form.
  • In the Name field of the Edit Library form, enter "Panorama Human Library".
  • Click on the Browse... button.
  • Select the "Human_rev3.clib" chromatogram library file that you downloaded earlier.
  • Click the OK button in the Edit Library form.
  • Click the OK button in the Edit Libraries form.
  • Check the box next to "Panorama Human Library", in the Libraries list.
  • In the Pick peptides matching dropdown list that appears, select Library (if it is not selected by default).
  • In the Rank peptides by dropdown list, select Peak Area.
  • Check the Limit peptides per protein box.
  • In the Peptides field, enter "5".
The Peptide Settings form should now look like this:

  • Click the OK button.
The number of transitions in the document should have decreased from 220 to 64. Skyline also displays a rank for each peptide as indicated in the image below. This rank is based on the total peak area, summing all transition peak areas, for the peptide in the library.

This number can be further reduced by limiting the transitions to the top ranking transitions in the library.

  • On the Settings menu, click Transition Settings....
  • Click the Library tab.
  • Check the box for If a library spectrum is available, pick its most intense ions.
  • In the Pick: product ions field that appears, Enter "3".
  • Select the From filtered product ions option.
The Transition Settings form should look like this:

  • Click the OK button.
The number of transitions in this document should now be 30.

You can now export a transition list or a native instrument method for this document, and acquire data. Skyline offers the ability to export transition lists and SRM methods for instruments from several different instrument manufacturers.

  • On the File menu, choose Export and click either Transition List... or Method....
  • To view the list of supported instrument types, use the Instrument type dropdown menu.
Please see the Targeted Method Editing and Targeted Method Refinement Skyline tutorials for more information on exporting transition lists and SRM Methods.

The files you downloaded for this tutorial already contain a document with data acquired on a triple quadrupole mass spectrometer. To begin exploring how acquired data and your new chromatogram library can be used together:

  • Open the file "In_vivo_versus_in_vitro_comparison.sky" in Skyline.
  • In the Targets view, select the peptide "TFQCELCSYTCPR", under the CTCF protein.
The Skyline window should look like this:

You should see the chromatograms for this peptide from the newly acquired data side-by-side with the chromatograms from the Human_rev3.clib library. The tab titled K562 (nuclear) has the chromatograms from the new data, and the tab titled Library Match displays the library chromatograms.

If you do not see the Library Match tab you can display it as follows:

  • On the View menu, click Library Match.
Skyline also calculates a dot product as a measure of similarity between the peak areas in the new data and the library peak areas. This is displayed next to the precursor, as marked in the image above. For the peptide TFQCELCSYTCPR the similarity is high, with a dot product of 0.97, and that gives a measure of confidence in the peptide identification.

Conclusion

In this tutorial, you have gone through the steps of creating a library folder in Panorama for curated, targeted results. You have built a chromatogram library in Panorama, and used it in Skyline to select the peptides and product ions to measure in a new experimental setting. You have also compared chromatograms acquired in a new experiment with data contained in the library to validate peptide identifications. By using these techniques with your own experimental data, you can build an extensive knowledge base of the targeted assays you have investigated and refined in your laboratory, and avoid duplicating this effort in new experiments. You can share these libraries with collaborators or the general public, as others are already doing, helping others to reproduce your results, or use them for new applications in targeted proteomics.

Reference List

1. Stergachis, A., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J., Rapid empirical discovery of optimal peptides for targeted proteomics Nature Methods 8,1041–1043 (2011)

Related Topics




Tutorial: Submitting Supplementary Data to Panorama Public


Overview

PanoramaWeb (https://panoramaweb.org), the public Panorama server hosted at the University of Washington is being increasingly used by researchers to host data processed in Skyline for sharing with collaborators and for referencing in published papers. Users on PanoramaWeb are given their own projects over which they have full administrative control. The ease of uploading Skyline documents to Panorama combined with the ability to configure permissions and folder structure makes PanoramaWeb an attractive choice for hosting and sharing data from Skyline centric workflows. It also makes it possible for users to provide public access to data for fulfilling journal submission requirements. Several papers have already been published that reference supplementary Skyline documents hosted on PanoramaWeb. However, data in user projects remains under the control of the user, and may be edited or deleted post publication.

To address this concern, PanoramaWeb now hosts a public repository called "Panorama Public" where users may submit supplementary data contained in their projects on PanoramaWeb. The repository provides a permanent location for data to be referenced in publications. Upon submission, a copy of the data contained in the user project is made to Panorama Public. This copy includes user interface elements such as wiki pages, charts and other supplementary figures which were added by the user to their project. Data copied to Panorama Public is read-only, ensuring its availability in the original form accepted for publication. Permissions to the data in Panorama Public are managed as required -- private with access to reviewers while the manuscript is in review and public after the paper has been accepted.

In this tutorial you will you will prepare a folder on PanoramaWeb for submitting to Panorama Public. This will involve uploading documents related to a manuscript and building a custom user interface around the data. Finally, you will go through the steps of submitting the folder to Panorama Public. A large part of this tutorial covers adding custom user interface elements to enhance the presentation and provide context to the supplementary data contained in a folder on PanoramaWeb. If you already have a folder that is ready for publication, you can skip to the section "Submitting to Panorama Public" that covers the steps required for submitting data to Panorama Public.

In this tutorial you will use several features that are part of LabKey Server (https://www.labkey.org), the data management platform behind Panorama, to create a user interface for your supplementary data on PanoramaWeb. Links to detailed documentation provided by labkey.org on individual features are included in the tutorial in yellow boxes like the one below. Please note that these links are not part of the tutorial and are only meant to provide more detailed information on a particular feature in LabKey Server. The link below takes you to the main documentation page on labkey.org.

Getting Started

To start the tutorial, download the following ZIP file:

Extract the files to a folder on your computer, like:
C:\UsersYour_Username\Documents

This will create a new folder:

C:\Users\Your_Username\Documents\SubmitToPanoramaPublic

It will contain all the necessary files for this tutorial.

The data used in this tutorial was published in Abbatiello et al. 2013, where the authors described a system suitability protocol (SSP) that helps to ensure reproducible analyte quantification measurements within a lab or across multiple laboratories with different MS instrument platforms. The SSP was evaluated in 11 laboratories on a total of 15 different instruments, and the data analyzed in Skyline. The resulting Skyline documents were uploaded to PanoramaWeb and made publicly available at:

The data for this tutorial contains Skyline documents from 3 of the participating laboratories, of which one used a ThermoFisher TSQ Vantage instrument and the other two used the SCIEX 4000 QTRAP instrument.

In the following sections you will:

  • Create a folder on PanoramaWeb and upload Skyline documents to the folder.
  • Add wiki pages with text, supplementary figures and tables.
  • Prepare the folder for submission by providing an abstract, organism, instrument information etc.
  • Submit to Panorama Public.

Signing Up for an Account on PanoramaWeb

This tutorial assumes that you will be working in a sub-folder of the "Tutorials" project on PanoramaWeb, the Panorama server hosted by the MacCoss lab at the University of Washington. However, if you already have a project on this server, you are welcome to work in a sub-folder of your project, and skip to the next step.

To request a folder on PanoramaWeb for working through this tutorial, fill out the sign-up form on this page:

Once your request is approved, a folder with full administrative rights will be created for you in the "Tutorials" project on PanoramaWeb. You will also receive a welcoming email with a link to complete your account registration by choosing a password.

Creating a Folder in Panorama

Sign in to PanoramaWeb at https://panoramaweb.org with your username and password. If you are working in the "Tutorials" project follow these steps to navigate to your folder under this project:

  • Click the Projects tab in the upper right corner (shown below) to see a list of all the projects to which you have access on the server.
  • Click the "Tutorials" project.
  • On the project homepage, hover over the project name in the menu bar below the Panorama icon and click on the folder that was created for you. We will use "Your_Username" as the folder name only as an example. Your folder name will be different.

NOTE: Most of the Panorama features that you will explore in the rest of the tutorial require that you have administrative permissions in the folder that you are working in. If you are working in your sub-folder in the "Tutorials" project you are the administrator of the folder. If, however, you are working in another project on PanoramaWeb you must contact your project administrator to ensure that you have administrative permissions.

You will now create a subfolder where you will upload Skyline documents and add other supplementary information for a manuscript. To create a sub-folder for this tutorial, do the following:

  • Click the new folder icon shown in the image below.
  • In the Create Folder form, enter "System Suitability Study" in the folder Name field.
  • Select the Panorama option under Folder Type, as shown below.
  • Click the Next button.
  • On the Users/Permissions page accept the default selection (Inherit From Parent Folder).
  • Click the Next button.
  • On the Configure Panorama Folder page accept the default selection (Experimental data).
  • Click the Finish button.
After successful folder creation, you will be taken to the home page of the "System Suitability Study" folder. You are now ready to upload Skyline documents to this folder.

Uploading Skyline Documents to Panorama

From the tutorial files downloaded earlier, open the "Study9S_Site52_v1.sky" file in Skyline either by double-clicking on the file in Windows Explorer or in Skyline, on the File menu, click Open (Ctrl-O). This file contains measured results for 22 peptides from one of the participating labs in the system suitability study (Abbatiello et al. 2013). To upload this document to the folder you just created on Panorama, follow these steps:

  • Click on the Upload to Panorama button in the Skyline toolbar, shown in the image below. Alternatively, on the File menu, click Upload to Panorama.

If you have not yet set up a Panorama server in Skyline, you will see the following message.

  • Click the Continue button.
Do the following in the Edit Server form:
  • Enter "https://panoramaweb.org" in the URL field.
  • Enter your email address and password on PanoramaWeb.
  • Click the OK button.
Skyline will display a Upload Document form with the folders available to you on PanoramaWeb.

  • In the Panorama Folders field, navigate to and select the "System Suitability Study" folder that you just created on Panorama.
  • Click the OK button.
Wait for the document import to complete. When asked whether you want to view the file in Panorama, click No. Follow the same steps to upload the other two Skyline files in the tutorial data – "Study9S_Site56_v1.sky" and "Study9S_Site65_v1.sky" to your "System Suitability Study" folder on PanoramaWeb.

Once all three documents have been imported into Panorama, go back to the web-browser where the home page of the "System Suitability Study" folder should still be open. Refresh the page (F5 in most browsers) and you will see the three files that you just uploaded in the Targeted MS Runs table.

Customizing Grid Views in Panorama

Click on "Study9S_Site56_v1.sky.zip" in the Targeted MS Runs table to open the details page for the document. The Precursor List table on this page displays a list of precursors in this Skyline document. The Precursor Note/Annotations column in the table, highlighted in the image below, is blank since the researchers did not define any custom precursor annotations in this document.

Do the following to hide this column from the default grid view:

  • Click the (Grid Views) button at the top of the table, just under the Precursor List title.
  • Select Customize Grid from the drop-down menu.

In the customization form that appears, you will see a Selected Fields panel, to the right, that lists the columns that are currently displayed.

  • Scroll down, then hover over Precursor Note/Annotations below Precursor in the Selected Fields panel and click the (remove) icon.
  • Click the Save button.
  • In the Save Custom View form, check Make this grid view available to all users.
This will ensure all users with access to this folder see the same table columns.
  • Click the Save button.

The Precursor Note/Annotations columns should no longer be displayed, as shown below:

Go back to the home page of the "System Suitability Study" folder by clicking on the folder-name link near the top of the page as shown here:

TIP: This folder name link is provided on all pages within the folder except the main home page and provides a quick way to navigate to the home page of that folder.


Click on "Study9S_Site52_v1.sky.zip" in the Targeted MS Runs table. The default view for the Precursor List table for this document should not have the Precursor Note/Annotations column. Custom grid views defined once in a folder apply to all Skyline documents uploaded to the folder. The "default" grid we saved our changes to is shown by default.

Creating Wiki Pages on Panorama

Wiki pages allow you to add content, including file attachments, to your folders on Panorama. You will now create a wiki page to display a supplementary figure (Supplementary Figure 3A) from the original paper along with a figure caption. This figure displays normalized peak areas for the 9 best peptides identified in the study (Abbatiello et al. 2013), across 10 replicates in each site. The original figure has a plot for each of the 15 sites in the study. "SupplFig_3A.png" in the tutorial files has plots for the 3 sites for which Skyline files are included in the tutorial.

Navigate back to the "System Suitability Study" folder home page. To add a wiki page in the folder, we first need to enter "Page Admin Mode" to add a new wiki web part to the folder page.

Do the following:

  • In the header, click the (gear) icon to open the Admin menu. Select Page Admin Mode.
  • From the <Select Web Part> drop-down menu that will appear at the bottom left of the folder home page, scroll down and select Wiki.
  • Click the Add button.

A box titled Wiki will be added under the Targeted MS Runs box that should look like this:

  • Click the Create a new wiki page link to open the wiki editor.
  • Enter "supplementary_figure_3A" in the Name field. The name must be unique in the folder and typically does not contain spaces.
  • Enter "Supplementary Figure 3A" in the Title field. The title is the display title and has no restrictions on uniqueness or spaces for display.
  • In the Body (HTML) field select the Visual tab if it is not already selected.
  • In Notepad or another text editor open the file "SupplFig_3A_caption.txt" contained in the tutorial data you downloaded. Copy and paste the contents of this file into the Body (HTML) field.
  • You can format the text using the options available in the formatting toolbar. - Remove any preformatting by selecting the text and choosing the format "Paragraph".
  • Select the title of the figure caption ("Supplementary Figure 3A") and make it bold by clicking the B button in the toolbar. You can see more formatting options in the toolbar by clicking the Show/hide toolbars button at the left corner of the toolbar.
  • Upload an image file to display on the wiki page:
    • Scroll down, if you need to, to the Files field at the bottom of the wiki editor.
    • Uncheck the Show Attached Files checkbox.
    • Click the Attach a file link and click the Choose File button that appears.
    • Navigate to the folder where you downloaded the tutorial data and select "SupplFig_3A.png".
    • Click on the Open button.
  • Add the image to the wiki page:
    • Place the mouse cursor just before the figure title in the Body(HTML) field.
    • Click the Insert/edit image icon in the toolbar.
    • Enter "SupplFig_3A.png" in the Image URL field of the Insert/edit image dialog.
    • Click Insert in the dialog.
    • Press the "Enter" key on your keyboard once so that the image title is below the image icon in the Body(HTML) field. At this time the actual image will not appear in the editor.
The Body (HTML) field should look like this:

  • Click the Save & Close button at the top left of the wiki editor.
You will be taken back to the "System Suitability Study" folder home page. You should see the wiki page that you just created at the bottom of the page. It should look like this:

A note about "Web Parts" in LabKey Server:

The wiki page that you just created appears on the folder home page in a box with a border and a title that is referred to as a "web part". Web parts are user interface panels that can be added or removed from folder pages by folder administrators when they are in page admin mode. Each web part provides a way for users to view and/or interact with some part of the data contained in the folder. For example, the Wiki web part displays the contents of a specific wiki page. The list of available web parts can be accessed from the two <Select Web Part> menus at the bottom of the folder home page – one on the left side and the other on the right side. The two menus have different sets of available web parts. Web parts selected from the menu on the bottom left of the page are wider and get added to the left side of the page, and those selected from the menu on the bottom right get added to a narrower column on the right side of the page.

The title bar of a web part has controls (available to folder administrators in page admin mode) for moving it up and down the page, relative to other web parts. These controls appear in the right side of the title bar for the wider web parts, shown in the image below.

The term "web part" will be used in the remainder of the tutorial to refer to these user interface elements.

You will now add a table of contents for easy navigation to the wiki pages.

  • Scroll down to the bottom of the page.
  • Choose Wiki Table of Contents from the <Select Web Part> drop-down menu at the bottom right of the page.
  • Click the Add button.
This will add a narrower web part titled Pages to the right side of the folder home page as shown below. Links to all the wiki pages that you add in this folder will appear in this web part.

  • Change the title of the web part by clicking the (triangle) drop-down icon in the title bar and selecting Customize. If you are still in page admin mode, you will see additional options on this menu.
  • Enter "Figures & Tables" as the title (leave the folder path as is) and click the Submit button. The table of contents web part on the home page should now display the updated title. This webpart will allow you to easily navigate to all the wiki pages in this folder as you add additional figures and tables in new wikis.
You will now create another wiki page where you will add a supplementary Excel table containing the retention time drift information. This table has been taken from the original paper and data filtered to the three sites for which Skyline files are included in this tutorial.
  • Add a new wiki page by clicking the drop-down icon in the title bar (which should now read Figures & Tables) of the Wiki Table of Contents web part.
  • Select New from the menu.
Do the following in the wiki editor:
  • Enter "supplementary_table_6" in the Name field.
  • Enter "Supplementary Table 6" in the Title field.
  • In the Body (HTML) field select the Visual tab if it is not already selected.
  • In Notepad or another text editor open the file "SupplTable_6_caption.txt" contained in the tutorial data. Copy and paste the contents of this file in the Body (HTML) field.
  • Remove any preformatting by selecting the text and choosing the format "Paragraph".
  • Format the text using options available in the formatting toolbar. For example, you can make the title ("Supplementary Table 6") bold.
  • In the Files field at the bottom of the wiki editor click the Attach a file link and click the Choose File button.
  • Navigate to the folder where you downloaded the tutorial data and select "SupplTable_6.xlsx".
  • Click the Open button if double clicking does not attach the file and close the popup.
  • Notice that we are leaving the Show Attached Files checkbox checked this time.
  • Click Save & Close at the top of the wiki editor.
The new wiki page should look like this:

Viewers can click on the attached file to download it.

Notice that we did not create a new wiki web part for this wiki, so you are viewing the wiki page itself. By default, a search box and a Wiki Table of Contents web part with the title Pages is shown. This web part should display the titles of the two wiki pages you have in the folder. You can click on a title to view either wiki page.

Go back to the home page of the folder by clicking the System Suitability Study link near the top of the page. Notice on the home page that the Figures & Tables is displayed in the table of contents web part here.

Since the wiki pages can now be accessed via the table of contents web part, you can remove the wiki web part that is displaying "Supplementary Figure 3A" from the folder home page.

  • Scroll down, if you need to, so that the title bar of the wiki web part is visible.
  • From the (triangle) menu, select Remove From Page.
    • If you do not see this option, first reenter page admin mode by selecting: Page Admin Mode in the header.
  • Notice that the wiki itself is still available from the table of contents. Removing the web part did not remove the underlying content.

Submitting to Panorama Public

Folders containing supplementary data intended for publication to Panorama Public have to be annotated with a description of the experiment. This includes information such as an abstract, experiment and sample descriptions, organism, MS instruments used etc. To add experiment annotations to the folder, do the following:

  • Go back to the home page of the System Suitability Study folder, if you are not already there.
  • Re-enter > Page Admin Mode if you are not already in this mode.
  • Select Targeted MS Experiment from the <Select Web Part> menu at bottom-left of the page.
  • Click the Add button.

This action will add a web part titled Targeted MS Experiment at the bottom of the page that looks like this:

  • While in page admin mode, you can change the layout of the folder home page to move the Targeted MS Experiment webpart to the top of the page.
    • Move the Targeted MS Experiment web part above the Targeted MS Runs web part by selecting Move Up from the (triangle) menu in the web part title bar.
    • Scroll to the top of the page and remove the Mass Spec Search web part by selecting > Remove From Page in its title bar.
  • Click Exit Admin Mode at the top of the page to hide the page layout editing features.
Next, create the experiment:
  • Click the Create New Experiment link in the Targeted MS Experiment web part.
  • In the Targeted MS Experiment form enter "System Suitability Study" in the Title field.
  • Enter "TSQ Vantage, 4000 QTRAP" in the Instrument field
  • In Notepad or another text editor open the file "Abstract.txt" included in the tutorial data. Copy the contents of the file and paste in the Abstract field of the form.
  • Click the Submit button at the bottom of the form.

You will be taken to the experiment details page. All the Skyline documents you upload to this folder will get added to the experiment and will appear in the Targeted MS Runs table. In this tutorial you have uploaded all the Skyline files to a single folder. If, however, you wanted to organize your data in sub-folders under the "System Suitability Study" folder, you would click the Include Subfolders link shown in the image below.

Navigate back to the folder home page by clicking the System Suitability Study link near the top of the page.

To submit to Panorama Public, click the red Submit button in the Targeted MS Experiment web part.

You will be presented with a form that looks similar to the image below:

In the Submission Request to Panorama Public form do the following:

  • If you were working in a folder with real data for a manuscript, you would select "Panorama Public" from the drop-down list next to the Submit To option (it is the default, shown above). For this tutorial, select "Panorama Public Tutorial".
  • Enter "publication _tutorial_<your_ folder_name>" in the Access Link field. Replace <your_ folder_name> with the name of your folder in the "Tutorials" project. For example, if you folder name is "Your_Username" enter "publication_tutorial_Your_Username" in the textbox. The URL displayed below the textbox will be updated as you type in the textbox. Once you have finished typing the URL should read (for folder "Your_Username")
    https://panoramaweb.org/publication_tutorial_Your_Username.url
  • Uncheck the Keep Private checkbox. If you were submitting data for a manuscript undergoing peer review you could keep the Keep Private box checked. This will ensure that when the data is copied to Panorama Public, it will be kept private with read-only access to the submitter. Another read-only reviewer account will be created for the data, and account details provided to the submitter. These account details can be conveyed to the journal where the manuscript is submitted.
  • Click the Submit button.
The Access Link provided in the UI in bold is the link that you will include in your manuscript to link to supplementary data on Panorama Public that can be viewed in a web browser. Initially, this link points to your folder on PanoramaWeb. But once a copy of your data has been made to Panorama Public, it will link to the location of the copied data on Panorama Public. This will be the permanent location of your supplementary data on Panorama Public.

The Submission Request to Panorama Public form allows you to "build" this access link. The initial part of the link remains constant: https://panoramaweb.org/. You can choose a string to complete the link (highlighted in yellow below).

https://panoramaweb.org/choose_a_string.url

The initial value entered in the Access Link field is a randomly generated alphanumeric string. You can replace it with a convenient, easy to remember string. This string has to be unique across all the experiments submitted to Panorama Public. You may get an error if the link you entered is already in use for another experiment on Panorama Public. If this happens change the text and try again.

When the form is submitted successfully you will be taken to the experiment details page.

In the Experiment Details box, you will see a red "Copy Pending!" message, circled below. This message will disappear once your data has been copied to Panorama Public. Any changes that you make in the folder, such as adding/removing Skyline documents or wiki pages, or changing the layout of the page will also get copied when a copy is made to Panorama Public. At the bottom of the page, in the Submission table, you will see the Access Link that you created for this experiment. The Copied column, circled below will be blank until a copy has been made successfully.

Once the data has been copied this column will display the date when the data was copied. You will also receive an email informing you that the data was successfully copied to Panorama Public. At that point if you click on the value in the Access Link column you will be taken to the folder where your data was copied on Panorama Public and you can verify that the data, folder layout, and views were copied accurately.

Requests to copy data are handled by Panorama Public administrators within a week of submission. Once your data has been successfully copied to Panorama Public you will receive a confirmation email. If you requested that your data on Panorama Public be kept private (e.g. for a manuscript under peer review), the confirmation email will also include reviewer account details. You can pass on the account details to the journal where you are submitting your manuscript.

Reference List

1. Abbatiello, S. E., Mani, D. R., Schilling, B., MacLean, B., Zimmerman, L. J., Feng, X., … Carr, S. A. (2013). Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS). Molecular & Cellular Proteomics : MCP, 12(9), 2623–2639. doi:10.1074/mcp.M112.027078

On Oct 20, 2015, the Skyline and Panorama Teams produced Webinar #11: Panorama Public and Panorama AutoQC, another great resource to learn more about some of the new aspects of Panorama.



Webinars


Panorama Webinar hosted by LabKey (September 21, 2017) Introduction to Panorama 17.2

Skyline Webinar #11 (October 20, 2015) Panorama Public and Panorama AutoQC

Webinar August 19, 2014
Panorama: Managing and Analyzing Large Datasets

[slides]

Webinar August 8, 2013
Panorama targeted proteomics knowledge base

New features in Panorama v13.2.

 

Webinar February 7, 2013
Panorama: An Introduction

An introduction to using PanoramaWeb.




Panorama: An Introduction


Webinar February 7, 2013
Panorama: An Introduction

An introduction to using PanoramaWeb.




Panorama Targeted Proteomics Knowledge Base


Webinar August 8, 2013
Panorama targeted proteomics knowledge base

New features in Panorama v13.2.




Panorama: Managing and Analyzing Large Datasets





Panorama Public and Panorama AutoQC


Skyline Webinar #11 (October 20, 2015)
Panorama Public and Panorama AutoQC




Introduction to Panorama 17.2



Panorama Webinar hosted by LabKey (September 21, 2017) Introduction to Panorama 17.2




Publications


Peer reviewed manuscripts

  • Panorama: A Targeted Proteomics Knowledge Base. Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. Journal of Proteome Research. 2014
    [abstract][pdf]
  • Panorama Public: A public repository for quantitative data sets processed in Skyline Vagisha Sharma, Josh Eckels, Birgit Schilling, Christina Ludwig, Jacob D. Jaffe, Michael J. MacCoss and Brendan MacLean. Molecular and Cellular Proteomics. 2018
    [abstract]
  • An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments Michael S. Bereman, Joshua Beri, Vagisha Sharma, Cory Nathe, Josh Eckels, Brendan MacLean, Michael J. MacCoss. Journal of Proteome Research. 2016
    [abstract] [pdf]

Posters

  • Managing Small Molecule Targeted Mass Spec Assays using Skyline and Panorama. Eckels J, Sharma V, Pratt B, Dunkley T, Wildsmith K, Anania V, Li Q, Nathe C, Patel B, MacCoss MJ, MacLean B. ASMS Poster. 2016
    [pdf]
  • Performing quality control on targeted proteomics assays using Skyline and Panorama. Eckels J, Sharma V, Boss Y, Shi H, Dunkley T, Wildsmith K, Nathe C, Robinson A, Johnson R, Jaffe JD, MacCoss MJ, MacLean B. ASMS Poster. 2015
    [pdf]
  • Panorama Public: A public repository for Skyline documents. Sharma V, Eckels J, Schilling B, Jaffe JD, MacCoss MJ, Brendan MacLean. ASMS Poster. 2015
    [pdf]
  • Sharing targeted proteomics assays using Skyline and Panorama. Eckels J, Sharma V, MacLean B, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Jaffe JD, MacCoss MJ. ASMS Poster. 2013 [pdf]
  • Panorama: A Private Repository of Targeted Proteomics Assays for Skyline. Sharma V, MacLean B, Eckels J, Stergachis AB, Jaffe JD, MacCoss MJ. ASMS Poster. 2012 [pdf]



Dashboard


Projects on PanoramaWeb
PanoramaWeb currently hosts projects for labs.
Skyline Documents on PanoramaWeb
Skyline documents have been uploaded to PanoramaWeb.



Example Data


See example experiments on PanoramaWeb

Yeast SILAC data from MRMer experiment (Martin, D. B., et al.)

• Data from inter-laboratory studies of the CPTAC Verification Working Group (Addona, T.A. et al.)

Assays for human transcription factors (Stergachis, A.B. et al.)

Rat heart study data (unpublished)

Analysis of cross-linked peptide pairs using small molecule data - (Chavez, J.D. et al.) (also view in Panorama Public)

Quality Control example using data from the SProCoP tutorial

Quality Control example using data published in An Automated Pipeline to Monitor System Performance in Liquid Chromatography Tandem Mass Spectrometry Proteomic Experiments.

Quality Control example using data published in MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments.

Quality Control example using Lindsay's real world QC data

Developers with experience creating SQL queries, R, Perl, Python or other scripts may be interested in exploring the Query Schema Browser to see the underlying data structures exposed for SQL queries, especially the queries in the targetedms schema, or LabKey Server client API requests.




Related


Skyline
Learn more about Skyline software for large-scale proteomics studies.

LabKey Server
Learn more about LabKey Server open source tools for biomedical research from LabKey.




University of Washington