Mass Spectrometry Core Data Files

Viewing Data

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

Docx, xlsx

docx, xlsx files are created in Microsoft Office with xml format files. 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 2010 or 2013 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. If needed, data can be supplied as a text file, with paired values for mass and intensity which can be opened in Excel or other program.

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 190MB download in 2015.

Note the installation requirements at:
http://www.proteomesoftware.com/pdf/system_requirements.pdf

We have found that large files, 1G or larger, often fail to open on machines with <8 GB memory. Multi-core processors help as does 64 bit operating system.

Go to Products, select Scaffold. Do not choose a trial version if offered. After Installation, in the Opening window, click on Viewer Mode in the bottom right corner.

Viewing data

Scaffold has a 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. Some image editing programs, such as Adobe Photoshop and Irfan View, can save pdf files as JPG and other image file formats.