Sample submission for mass spectrometry

Proteus LIMS

  1. Web based. 
  2. Project status updated with progress. 
  3. Results in electronic format posted to the project 
  4. Data can be shared with people you chose
  5. Data stored on Proteus LIMS. 

MALDI Sample preparation

  • 10 pmole/µL or more desired
  • 5 or more µL
  • SDS incompatible
  • Other detergents can cause problems but special procedures may get data
  • molecules <600 may be obscured by matrix
  • knowing purpose of experiment can be helpful

Samples for protein identification

  • If supplying gel bands, bring whole gel
  • Detergents need removal
  • Contamination by skin keratin is a common problem
  • Only some silver stains are compatible with mass spectrometry

Using Proteus system

To login to submit samples or retrieve your data, go to:
http://proteus.achs.virginia.edu:8080/lablink/Welcome.do

You can fill out a form for an individual sample, or fill out a spreadsheet which you upload. The spreadsheet is Microsoft Excel (.xls) format.  If there are error messages, sample information will not transfer into the Proteus system.

Delivering samples 

  • Complete sample information in the Proteus system.
  • Give sample tubes unique names
  • Bring to room 1105 Jordan Hall
  • If submitting gel bands, bring the whole gel and a picture showing the bands or spots to be analyzed.
  • If shipping the gel from outside the University of Virginia, we suggest sealing it in a bag placed between sheets of cardboard for protection. Send samples to:
    Dr. Nicholas Sherman
    Department of Microbiology, Box 800734,
    University of Virginia Health System,
    1300 Jefferson Park Avenue
    Charlottesville, VA 22908-0734
    (phone 434-924-0070)

Getting your data  

Starting with Proteus 

To start, you will need an account which can be requested at:
http://128.143.19.247:8080/lablink/NewClient.do?new=1
If you have already received data through Proteus (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. 

Detailed descriptions and directions for Proteus are at:
http://proteus.achs.virginia.edu:8080/GLS/help.do

To submit sample data, after logging on to Proteus, you can fill out a form for an individual sample, or fill out a spreadsheet which you upload. The spreadsheet is Microsoft Excel (.xls) format.  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.

Copying data from pdf files to other programs.

MALDI data is supplied as pdf files.

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.
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.

PDF Creation programs such as Adobe Acrobat (not reader) can save pdf files in different formats, such as tiff and other image file formats. For information about purchasing a license for Adobe Acrobat through Research Computing Services, see:
https://www.web.virginia.edu/rescomp/SoftwareInfo.asp?ID=23
Free pdf creation programs can be found on the web and may suffice for simple use.