Embryonic Stem Cells
The IMol's Proteomic Core Facility

The IMol's Proteomic Core Facility is a specialised laboratory dedicated to measure and analysis of peptides and proteins unique for biological processes and structures. Currently, the lab is equipped with an nanoLC Dionex Ultimate 3000 copuled with Q-Exactive HF-X mass spectrometer.

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EQUIPMENT

nLC-coupled Q-Exactive HF-X

  • This hybrid quadrupole-orbitrap instrument constitutes a high-performance platform for both bottom-up and top-down proteomics studies. Advanced scanning modes featuring improved peak-picking and the new ultrafast MS/MS scan time below 20 milliseconds yield great improvements in polypeptide sequencing speed and depth.

  • Bottom-up proteomics utilizes digestion of proteins into peptides which are then sequenced in the mass spectrometer and act as surrogates for the presence of proteins from which they are derived. Besides insights into protein expression levels and the extent of posttranslational modifications, this mode of analysis can be applied to provide information about protein turnover, subcellular localization, as well as protein-protein and protein-small molecule interactions.

  • During top-down proteomics full length proteins are measured and fragmented in the gas phase to deliver information about the amino acid sequence and modifications covalently attached to them. Proteoform - level resolution is achieved by this mode of analysis.

PRICELIST

Ceny dla klientów/partnerów zewnętrznych

Pomiary popularne:

  • Próbka (sam pomiar i podstawowa analiza danych, bez preparatyki).         250 PLN

  • Próbka LFQ/SILAC ze standardową preparatyką (od 8 próbek)300 PLN

  • Próbka ze standardową preparatyką i znakowaniem TMT (od 10 próbek)415 PLN

  • Pomiary wymagające wzbogacania peptydów/białek:

  • Próbka poddana wzbogaceniu fosfopeptydów i znakowaniu TMT (od 10 próbek)370 PLN

  • Próbka poddana wzbogaceniu biotynylowanych peptydów/białek i znakowaniu TMT (od 10 próbek)370 PLN

  • Próbka poddana wzbogaceniu peptydów modyfikowanych posttranslacyjnie (innych niż fosforylowanych) i znakowaniu TMT (od 10 próbek)od 370 PLN

  • Ceny zawierają opracowanie wyników pomiarów w wersji podstawowej (wyniki dostarczane w formie tabelarycznej).

  • Pomiary niestandardowe:

  • Szacowanie indywidualne.

 

  • Usługi dodatkowe:

  • Szczegółowa analiza danych (za godzinę pracy) 100 PLN

  • Pomiar stężenia białka – na wypadek próbek o nieznanym stężeniu (za próbkę) 25 PLN

  • Wszystkie ceny przedstawione na tej stronie są cenami netto.

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  • Zainteresowanych proszę o kontakt:

  • 22 55 43 679

  • r.serwa@imol.institute

GENERAL RULES

 

A formal acceptation of the rules and regulations is required prior to granting access to core facilities equipment and staff consultations. All information about them you can find in the form below:

 

General rules for the use of the CeNT UW Proteomic Core Facility nLC-coupled Q-Exactive HF-X:

General
1. The equipment is localized in room 06.105 in the CeNT I building.
2. Supervisor: Dr Remigiusz Serwa (E-mail: r.serwa@imol.institute)
3. Direct use of the nLC-coupled Q-Exactive HF-X is restricted to operators from within the core facility
4. Users are requested to submit a brief experiment proposal and obtain acceptance from the core facility head prior to sample preparation and measurement scheduling.
5. Users are obliged to familiarize themselves with these rules and confirm this fact by clicking the accept icon below.

Project submission
6. The submission of experiment proposals is made through https://warsaw-cent.calpendo.com/

Sample preparation
7. Users are required to follow sample preparation protocol approved by the facility head. Any modifiation (e.g. resulted from a human error) should be reported before the samples are handed over for the measurement. User who are discovered not to stick to this important rule, will be banned from submitting samples.
8. Internal (UW) users will be offered participation in a samples preparation workshops, during which they will be able to practice protein sample handling steps from cell extracts to desalted/fractionated tryptic peptide mixtures ready to be analysed by nLC-MS/MS. These will be advertised via email.

Provided services
9. The services offered by the core facility will be adapted to the
users’ needs. The services are being described in the current Pricelist. They include the following:
a. Consulting services (help with experimental design, customised sample preparation protocols, and post-experiment recommendations)
b. Sample measurement
c. Data analysis (basic processing as well as tailored analysis and data visualisation are avaialble)
10. Users are reminded that a brief or a detailed consultation, depending on their experience level, is expected to precede any measurement. During the consultation the most optimal analytical strategy is agreed and the estimated cost of services (calculated based on the Pricelist) is provided and explained. Before the measurements are being conducted, the user agrees to cover the cost.
11. The core facility staff is responsible for scheduling the services. Generally, user requests are being processed on a first come, first served basis. In justified cases (e.g. optimization of instrument usage or to ensure the reproducibility of serial measurements) an exception can be made and a divergent scheduling order may be applied.
12. The core facility headreserves the right to reject requests for the provision of services in objectively justified cases. In the event of a refusal, a constructive feedback will be provided. Head of the lab from which the proposed project originated will be notified about such a rejection, too.

Data storage & security
13. The results are being made available to the users in adequate form (e.g.: e-mail, cloud).
14. Raw data (spectra and database search results) are to be stored on a server. On request, they will be made available to the user.
15. Users are expected to collect data within 3 months from the time the results became available to them. After that time, access to the data will require intervention of the head of the lab, from which the project originated.

Publication of data
16. Acknowledgment: For basic analyses, where a minimal intellectual contribution from the core facility staff has been requested, their work should be clearly identified in the acknowledgments section of resulting publications. Protein/peptide lists will be provided along with a generic statement about the instrumentation and the search engine utilized.
17. Co-authorship: When a significant intellectual contribution from the core facility staff has been requested and delivered, their work must be acknowledged by naming them as co-authors of resulting publications. This is a default mode of agreement for projects involving development of new proteomic methods or projects requireing complex data processing and/or mining. A selection of publication-ready figures and an input into writing of the relevant sections of the paper will be provided.

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ATTACHMENTS

Internal Order Form to be completed and signed by non-ReMedy internal CeNT/UW users prior to making reservation assignments.

Internal User Order Form

 

External User Order Form to be completed and signed by external academic or external non-academic users prior to making reservation assignments.

External User Order Form

PROTEOMITYC CORE FACILITY FORM

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