The Mass Spectrometry Shared Resource (MSSR) is part of the CSHL Cancer Center, and it supports its collaborators with biological mass spectrometric analyses and with other biochemical measurements. The primary mission of the MSSR is to produce high-quality, interpretable and publishable mass spectrometry data, and to develop analytical capabilities required to address the scientific programs of our collaborators.

The MSSR provides our collaborators with specific expertise and advanced instrumentation that are not included in most research groups. We strive to understand the specific questions and experimental systems of our collaborators and leverage our expertise to design mass spectrometric experiments that are fit for the intended purpose. We operate as partners in advancing science, rather than providers of services on demand.

We provide most commonly used proteomics workflows, from identification of a recombinant proteins resolved by SDS-PAGE to quantitative analyses of non-canonical PTMs, crosslinking mass spectrometry, and other complex experiments. The lab has experience with several proteolytic reagents, all major approaches for peptide quantification (including label-free quantification, TMT, and SILAC), on- and off- line chromatographic separations, protein crosslinking and in situ biotinylation, quantitative analysis of phosphorylation and other PTMs.

The facility relies on high resolution orbitrap mass spectrometers that enable both data-dependent, targeted (PRM, SIM), and data independent acquisition strategies, and is equipped with ETD fragmentation and ion mobility interfaces.

We also leverage several platforms for data analysis, depending on the specific experimental design.

Importantly, the MSSR is eager to develop and/or implement new workflows as needed to address specific biological questions.

We begin all new projects by discussing the specific questions and experimental systems with our collaborators. During this meeting we collect relevant information (e.g., organism/expression system, available sample amount, etc.) and design the mass spectrometric experiment together. This process can be very quick and informal for simple projects (e.g., confirm the identity of recombinant proteins resolved by SDS-PAGE) or it may involve several meetings for complex experiments. Based on this discussion, we will suggest an appropriate experimental design (including number and amount of samples, buffers to be used, etc.). Complex projects that require the development of dedicated methods or performing pilot experiments will generally be divided into smaller projects, each aiming to address a specific question. We will deliver results for each project as they become available, and revise the experimental strategy based on these observations.

We will only accept samples once we are in the position to produce interpretable results (see “Mission”). For this reason, we deliberately do not use any standardized sample submission form. Because our resources and instrument time are limited, we may advise our collaborators not to perform an experiment if we believe that this will not produce any interpretable result (e.g. if critical controls are missing). We strongly advise against submitting de-identified samples (“blind experiments”), as this prevents us from running the analyses appropriately or efficiently.

We use sample preparation protocols designed to minimize downtime of our chromatographic and mass spectrometric systems. Collaborators that intend to autonomously prepare their samples for LC-MS analyses must discuss their protocols with our staff in advance, and we reserve the right to refuse injecting samples prepared outside of our facility if in our opinion they may interfere with MSSR instrumentation (e.g., if the sample contains detergents).

We welcome CSHL collaborators that want to use our facility to prepare their samples in our lab, using our protocols and tested reagents. In this case we train the researcher to navigate our lab and procedures, so that they can safely come and use our equipment and reagents to prepare their samples. We will provide all standard reagents, consumables, and apparatuses that are needed for sample preparation, and only bill the corresponding costs rather that the sample preparation fee. We will coordinate time slots with these collaborators based on other activities in the core, and until samples are ready to be injected, we will freeze them and analyze as instruments become available.

If samples prepared by our collaborators damage any component of our LC-MS, we will bill the cost of the components needed to fully restore functionality, and instrument time corresponding to the down-time for troubleshooting and QC (minimum 24h).

Instruments for proteomics analyses are only to be operated by MSSR staff.

Once we receive samples, we will perform the experiments as previously discussed, including data analysis, if required. As soon as the analysis is complete, we will provide a report containing:

  1. An overview of the experimental design and parameters;
  2. Relevant metrics for appropriate performance of the chromatographic and mass spectrometric instrumentation. This includes instrument blanks and method blanks (as applicable);
  3. Key LC/MS parameters;
  4. Summary of results to answer the original biological question(s) and aid interpretation of the data. This will also include experimental evidence to support the results (e.g. annotated MS spectra, etc.), as needed;
  5. Detailed experimental protocols for all biochemical procedures used.

We will also provide the original output of the proteomics software used and the results of subsequent data refining and analysis. Raw MS file will be available upon request.

We will store all files related to the experiments that we perform (reports, MS raw files, intermediated and processed data) for 5 years from the date we deliver the results, free of charge. Files will be stored locally in a CSHL operated server, with regular backup to ensure data safety.

It is the responsibility of our collaborators to obtain approval for experimental protocols involving human subjects or animals. The MSSR will not accept any sample and file containing any personally identifiable information or protected health information.

In general, we prioritize projects based on the sample intake date (first-in-first-out), with minor exceptions dictated by instrument availability and to maximize efficiency. Pending instrument availability, we aim to deliver results for simple experiments (<5 samples) within 10 days, and complex experiments within a month. We do our best to meet our collaborators’ deadlines (e.g. experiments included in grant proposals as preliminary results), but we cannot guarantee results by a specific date.

Projects from CSHL Cancer Center member groups are prioritized over other CSHL group and external collaborators.

We will support publication of the MS data that we produce by contributing to manuscript drafting and editing, producing relevant figures supporting MS data (within reasonable limit), and submitting dataset to external repositories (usually PRIDE).

Please acknowledge support of the NCI Cancer Center grant to the MSSR in all submissions including data produced by MSSR.

We encourage you to include MSSR staff members who contributed significantly to your publication as co-authors. This is particularly important in enabling us to recruit driven and motivated scientists to the MSSR.

We will bill each project shortly after the results have been delivered, usually at the end of the month. We manage our billing through the iLab platform, so we require collaborators to provide an iLab ID. We will bill every experiment that we perform, except for experiments that are not interpretable because of technical failure on our end.

Our fees are designed to recover the costs we incur and reflect the support that the MSSR receives from the CSHL Cancer Center and from CSHL. We use a modular fee structure that enables us to accommodate a wide range of experimental workflows, and to accurately reflect the work performed for method development. Experiments necessary to develop or implement a workflow not yet available at the MSSR will be billed as any other project. A discount will be applied to development of methods that will be of general use at the MSSR. We will address cost concerns during the initial design of the experiment, and try to minimize the cost for our collaborators, compatibly with recovery of our expenses. Support through shared funding and/or publication authorship do not affect our billing policies. All experiments carried out at the shared resource are collaborative in nature, and we expect our collaborators to cover the costs of their experiments.

We enthusiastically support our collaborators that plan to include mass spectrometric measurements in their grant proposals. The MSSR is available to review proposals, advise on specific experiments design, develop the corresponding budgets, and provide letters of support.

For proposals that include substantial collaboration with the MSSR, we strongly encourage our collaborators to include the corresponding costs in the budget and/or directly supporting the lab personnel as needed.

The MSSR is open for collaborations with users outside of CSHL, pending availability of resources and instrument time.