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The main goal of this study is to understand and pinpoint the main sources of variability and day-to-day arising issues faced by proteomics core facilities. The study is designed and divided into 2 sub-projects (Study A and B) that evaluate separately inter- and intra-laboratory variability. In the Study A, participants should analyze by LC-MS/MS a digest of yeast proteins using a pre-defined 150 minutes LC-MS/MS run. While in Study B, participants should perform their own sample digestion and then analyze it by LC-MS/MS (as in the Study A).
The study shall be carried on in 26 weeks. The final deadline to complete the study is December of 2011. Therefore, starting on the second week of May there is still 34 weeks left in 2011. The analysis must be run periodically and last at least 6 months. To cause minimal instrument burden to laboratories, participants can choose between two LC-MS/MS analysis schedules. Ideally, each participant should run the provided peptide sample once a week followed by 2 ‘blank’ runs. The alternative option is to run the sample (and blanks) once every two week. Once a month, the ‘in-house’ digested sample (study B) must be analyzed following the two blanks of the study A (see the ‘Run Order’ table on section 3). |
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1. Study samples: |
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Two sample tubes were sent to each participant laboratory. |
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- The unlabelled eppendorf contains 50 ug of trypsin-digested yeast protein.
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- The green-labelled eppendorf contains 150 ug of yeast protein.
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2. How to proceed |
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Upon receiving the samples, participants should prepare aliquots for the study A and study B. You will find a plastic bag with two tubes – protein sample (tube with a green tag on it) and peptide sample (tube not tagged) |
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3. LC-MS/MS analysis
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You are ‘free’ to choose most instrument method parameters; nevertheless, there are some rules that participants should follow in order to make posterior data analysis more feasible. |
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4. Data Availability
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All data generated for this study will be anonymized before making the results of the study public. The idea of carrying out this study has already drawn the attention of major proteomics initiatives that are interested in using the data for different purposes. Therefore, public availability of the data, in an anonymized form, is completely up to each participant. By default we consider that all data will be made available to the scientific community, if you do not want to do so, please let us know. Again, they will be anonymous!!!!! |
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Contact |
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Questions about this guideline should be addressed to Alex Campos (acampos@pcb.ub.es) and Eliandre de Oliveira (eoliveira@pcb.ub.es). |
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Agenda |
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Download |
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Presentation File |
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Download |
