Genologics LabLink

Genologics LabLink

The laboratory uses Genologics Proteus Laboratory Information Management System (LIMS).Users see this system through the LabLink interface.
To get an account with this system, go to:

http://proteus.achs.virginia.edu:8080/lablink/Welcome.do
and click the Request a User ID tab on the left side of the screen.
If you have already received data through LabLink (or submitted samples in the last three months), then use the login information already provided or contact the mass spectrometry lab to determine your login.

If you have forgotten your account information, contact the lab (434.924.0070) to determine your login. Names are case sensitive.

Proteus screen 1

Proteus screen 2

New users need to complete the sign up page as described in the directions listed above.

Sample Submission

To submit a sample, log on to LabLink and click on the Submit Samples tab on the left side of the screen (green outline in screen shot above).

Click on the link  Get instructions, forms and templates for submitting samples on the left side (red outline in screenshot above) to download an Excel file with examples and directions. Save file and upload.

If there are error messages, sample information will not transfer into the Proteus system.

If you have problems or questions, please contact the Keck MS Lab staff.

Viewing Data

To see your data, log in to GenoLogics LabLink. On the page which appears, in the drop down list next to View samples with status, select Invoiced and click the Apply box. Then click the Files tab.

Proteus screen 3

Several file types are familiar. Notes on some file types are below.

Docx, xlsx

docx, xlsx files are created in Microsoft Office 2007. A converter program from Microsoft will make most, but not all, features readable with earlier versions of Office at: http://www.microsoft.com/downloads/: look for Microsoft Office Compatibility Pack. After installing, run Microsoft or Office update to update the converter program.
At the University of Virginia, Office 2007 or 2010 can be installed under a Campus Agreement with Microsoft through ITS.

MALDI data

The standard way to store and send MALDI data is to print a spectrum to a pdf file. You can also export data to a text file, with paired values for mass and intensity; in the Bruker analysis program, go to File-Export-Mass Spectrum. To view the data, start MS Excel, select Open, select Text files as file type to open. Choose your file. You should have an option to designate the file type as Delimited. Click next, and select space as the delimiter. Your data should open with masses in one column, and intensity in another. The data can then be plotted in a chart.

Scaffold
.sf3, .sfd files

Files with extension .sfd or .sf3 were created with Scaffold.

Installation

You can download a viewer version of Scaffold software at:
http://www.proteomesoftware.com/
with versions for Windows, Apple OS, Linux; the Windows version is a 88MB download. Note the installation requirements at:
http://www.proteomesoftware.com/pdf/system_requirements.pdf

Scaffold has relatively frequent updates, including some changes in file format.
Reasons Scaffold does not work as expected include:

  • old version of program
  • presence of old program version in addition to current version
  • inadequate permission on folders (full control of ..\Program Files\Scaffold folder may not be sufficient)
  • Windows services Themes is running
  • Insufficient memory in computer

When you run Scaffold, you will see a Enter license key window.
Click the Free Scaffold viewer button.

  • Clicking on a file with extension .sfd/.sf3 will launch Scaffold (during Windows installations, Scaffold is set to open .sf3/.sfd files).
  • outside the University of Virginia, downloading the .sf3/.sfd file from LabLink, opening Scaffold and then opening the file may be necessary rather than automatically opening Scaffold within LabLink.
  • If Scaffold is running in a Windows limited user account, there may be an error message about lack of access to some files-it seems that this message can be ignored for viewing; giving limited users write permission on the \Program Files\Scaffold folder eliminates the messages. Version 3.2 and later seem to run in a limited user account.

Viewing data

Scaffold has a 78 page Users Guide which you can download under the help menu.
What data is displayed
If you have multiple samples of complex mixtures, they may all be displayed on the Samples page. To change the layout, go to the Load Data page
remove sample; use Save As to save the data set lacking one or more samples and preserve the original data set; this can be slow. On the tabs for the samples, right click for the delete option.
You can put samples in groups by right clicking the tab for the sample, and choosing Edit Biological Samples. In the Sample Category box, you can enter a name for a new group, for subsequent samples, you can choose the group name from the drop down list.
To hide the display of Biological Process-Cellular Compartment-Molecular Function go to View-Show GO Annotations and click to toggle the display.

pdf files

Copying data from pdf files to other programs


Text-Short sections:

In Acrobat Reader, point and click to select text. If that does not seem to work, go to Tools-Select & Zoom-Select Tool (Acrobat Reader version 8). In earlier versions, it may be a Text Tool.
Insert into document
The text will probably have the same formatting as the original text.
To have default formatting for text in Microsoft Word, use Edit-Paste Special-unformatted text (if this is a common operation, you can find or write to macro which can be assigned to a shortcut key).

Big blocks of text

In Adobe Acrobat reader 8, use File-save as text. Previous versions may be different.
The file will have extension .txt, no formatting. Each line with have a paragraph marker at the end.
To do a mass remove of paragraph markers, in Microsoft Word, use Find and replace command (Ctrl-h). For find what, enter ^p ( caret p as shown, not Ctrl-P)
For replace with, try nothing. If words are run together, undo change, and for replace with, press space bar once to replace paragraph markers with a space.
For these operations, it can be helpful to show formatting marks (In Word, Tools-Options, View tab, and select all formatting marks.)

Pictures

The snapshot tool will copy selected parts of a pdf file,  including a mix of text and pictures. In Acrobat Reader 8, go to Tools-Select &Zoom-Snapshot Tool. What is pasted is an image, so the text cannot be easily edited, or perhaps not edited at all.

Adobe describe methods for selecting an image only with the select tool and copying it. With the files produced from the MALDI software, currently these methods are unsatisfactory, giving rotated, distorted images which may only show in some programs.

PDF Creation programs such as Adobe Acrobat (not reader) can save pdf files in different formats, such as tiff and other image file formats. Free pdf creation programs can be found on the web and may suffice for simple use.