Services

FAQ

Sample Preparation and Submittal

Q1: Can the sample be submitted in either gel or liquid form?

A1: Samples can be submitted in either gel or liquid form for all services with the exception of intact protein molecular weight determination.

1a. Samples for intact protein molecular weight analysis should be in liquid form (i.e. in buffer solution). The buffer should not contain any detergent. Gel samples are not suitable because the intact protein cannot be extracted from gels efficiently.

1b. Gel bands submitted for other services should be cut into approximately 1 mm cubes. View schematic.

1c. Liquid samples for all other services can contain up to 4% SDS. If a liquid sample contains SDS, an additional fee for a FASP procedure will be added.


Q2: What is the sample submittal process?

A2: Fill out the online project request form, leave the samples in one of the two refrigerators in front of LTL 017. Include the sample transmittal form which was emailed to you when you submitted the request.


Q3: How much does it cost and how long will it take to get the results?

A3: An estimated cost and time will be displayed as you fill out the online form.


Q4: How can I find out the status of my project?

A4: When you submit a project request, a tracking number is displayed on the web page and is also included in the confirming email you will receive. Enter this number on the status page to track the progress of your project.


 Q5: Where is the sample drop-off place?

A5: There are two sample drop-off refrigerators (4 deg. C and -20 deg. C) in front of LTL 017 (next to the DNA sequencing sample drop-off and the IDT pickup location). Samples may be dropped off 24 hours/day, 7 days/week.


 Q6: Is it possible to discuss the project before submitting the sample?

A6: You are always welcome to discuss the project with us. Please contact Tharan (This email address is being protected from spambots. You need JavaScript enabled to view it., phone 8-3679) or Saw (This email address is being protected from spambots. You need JavaScript enabled to view it., phone 8-2210) or stop by the facility at any time (LTL 016).


Bioinformatics

Q1: Which database search engine do you use for protein identification?

A1: We use the Proteome Discoverer software with the built-in Sequest HT search engine for most data.  We will additionally use Byonic for phoso or glyco data.  We also have the Maxquant suite.


Q2: Can we get a copy of Proteome Discoverer?

A2: Proteome Discoverer can be downloaded from the Thermo portal: http://portal.thermo-brims.com/. After the free trial period of 30 days it can be used as Proteome Discoverer Viewer to analyze results in msf files.


Q3: How will the results be reported?

A3: Resultsl will be provide in a Scaffold file.  A free fully functional viewer is avaliable for download (http://www.proteomesoftware.com/products/qplus-s/download/).  Users may filter and manipulate their data as they see fit.


Q4: Where will the result be stored?

A4: Your "raw" MS data and Scaffold results files will be uploaded onto the OIT file server "lowrie".  For external collaborators, the Scaffold results file will be sent to you using SecureSend.


Q5: Where is Lowrie?

A5: Lowrie can be accessed at the locations show below, using your Princeton netID and password.  If you have not yet been given access to lowrie please contact MolBio IT Support at 8-2381 or This email address is being protected from spambots. You need JavaScript enabled to view it..


Windows:

Right-click on My Computer, and choose "Map network drive"

\\lowrie.princeton.edu\molbio\corefacilities\proteomics\lab-folder-name*

Mac:

In Finder, select Go => Connect to Server

Mac with Mac OS through 10.8.x:

smb://lowrie.princeton.edu/molbio/corefacilities/proteomics/lab-folder-name*

Mac with Mac OS 10.9.x (Mavericks), 10.10.x (Yosemite) or higher:

cifs://lowrie.princeton.edu/molbio/corefacilities/proteomics/lab-folder-name*

* Lab folders are named with the PI name followed by "lab", e.g. basserlab, schwarzbauerlab


Q6: Can raw data files be accessed?

A6: Raw data files will be uploaded to lowrie.