Brandeis University Mass Spectrometry Facility

Terms of Service

1. Services

The Brandeis Mass Spectrometry Facility provides analytical services for proteomics, metabolomics, and chemistry applications and develops new experimental protocols to extend the analytical portfolio for the Brandeis research community and external collaborators.

Contact

Brandeis University

Department of Chemistry

Dr. Fabian Schulte

415 South Street

Waltham, MA 02453

United States of America

E-mail: fabianschulte@brandeis.edu

Telephone: +1 781 736 2519

Our portfolio includes:

• Identification of Coomassie-stained protein bands from SDS-gels

• Identification and quantification of proteins in cellular extracts (label-free, SILAC, TMT)

• Quantitative analysis of post-translational protein modifications (e.g. phosphorylation, acetylation, ubiquitination)

• Analysis of protein interactions

• Identification and relative or absolute quantification of metabolites in complex samples (targeted and untargeted)

• De-novo sequencing of peptides

• Intact protein analysis

• MS1 and MS2 analysis of organic synthesis products

• Data analysis for the services listed above

• Scientific counseling for grant applications

2. Terms of usage

As there is no universal mass spec workflow, and experiment design and sample preparation very often have to be tailored for each individual scientific question, it is strongly advised to contact Dr. Fabian Schulte before you start a project. All projects and corresponding samples must be submitted using the sample submission forms, accessible from the facility website.

Our facility provides fee-for-service analysis for all Brandeis researchers as well as members of external academic research institutions and companies. Please contact Dr. Schulte for cost estimations. Although users have to pay fees for our services, charging does not preclude authorship on scientific manuscripts. For collaborative projects, any intellectual input, such as advice on experimental strategies and design, implementation of methods, data analysis, creation of figures, and manuscript proofreading, justifies a co-authorship on a manuscript that contains data generated in our facility.

The facility director reserves the right to refuse the retrieval of samples if quality standards are not met or the experimental design of the project was not agreed with the scientific personnel of the facility prior to the delivery of samples.

3. Priority of sample analysis

All samples will be processed and analyzed according to the date of sample handover to the technology platform. However, the TIMS-ToF instrument will be dedicated to nano-LC or UPLC operation in two-week shifts. Samples that require one or the other may have to wait until the appropriate LC is connected to be run on the TIMS-ToF.

In emergency situations, for example when additional data is needed before grant submission deadlines, exceptions may be made. The director of the facility will ultimately determine the order of samples in the existing queue.

4. Data analysis

The analysis of proteomics and metabolomics data is carried out by Dr. Schulte. Staff members of Brandeis University will also have access to a public data analysis workstation that is available in the laboratories of the platform to analyze their experimental results themselves. All MS files are archived on local servers and Box.com for backup and customers can have access to raw data upon request. The facility will provide scientific data in PowerPoint, Excel, vector graphics, or TIF image files. In some cases, the project requires considerable amounts of processing time to develop and run the MS analysis or extensive data analysis is required. For all these services, additional fees will be charged. Please contact us if you have any further questions.

5. Things to avoid

Mass spectrometers are very delicate devices and not all chemicals used in sample preparation procedures are MS compatible. Detergents and polymers (i.e., SDS) are the main source of ion suppression and have to removed completely from the samples, for example by SDS-PAGE or Acetone precipitation. Triton-X and Tween-20 are not allowed to be used, as these detergents cannot be eliminated from the samples by using dilution, washing, detergent spin columns, or SDS-PAGE and interfere severely with instrument performance. Please also avoid the use of corrosive compounds as they may damage the instruments. We do not accept samples that contain radioactive isotopes. If there remain any questions, do not hesitate to contact us.

6. Violation of rules

Upon submission of projects via this website the user accepts the terms of this statement. We reserve the right to reject future samples from analysis in case of violation of these guidelines.