Sample handling - call for participants
CAMPI 2 is a new Critical Assessment of MetaProteome Investigation (CAMPI) launched to establish a collaborative research program focused on methods for sample handling to preserve metaproteins function before microbiota analysis.
Organizers: Dirk Benndorf, Nico Jehmlich, Jean Armengaud, Robert Heyer, Felipe Bastida, Bob Hettich, Sergio Uzzau (“quarterback”), will coordinate the work of all volunteers from the Metaproteomics Initiative that would like to participate.
Participants: Labs with interest in metaproteome analyses.
Start date: December 2022 - Tentative end date: April 2023
One of the main challenges in metaproteomics studies is sample handling. Directly after sample collection, biological samples are shipped or stored at different temperatures, treated with preservation solutions or a direct protein extraction is performed. All these treatments lead finally to a different proteome profile which definitely influences the biological interpretation of your study.
The scope of CAMPI 2 is a comparative assessment of proteome sample stability after sample collection. Here, the most relevant issue is the sample treatment and the time spanning from sample collection to protein extraction (i.e., when microbiota composition and functions are challenged by short or long exposures to variations of temperature, humidity, pH, O2, etc.).
Volunteers will participate in applying their methods to stabilize the samples to be subjected to a real world “stress-test”, that will include the shipment with no control over temperature conditions.
The expected CAMPI 2 result is to provide a standard procedure for sample handling.
CAMPI 2 participants activities
Participants (pLabs) will be asked to suggest and apply a method for sample preservation. The method should be applied to either soil or fecal samples (or both) and must be provided by January 12, 2023.
Afterwards, 10 pLabs for soil and 10 for fecal samples, respectively, will be selected according to the criteria listed below. In addition to their provided method, pLabs will receive material and methods for 2 additional methods that will be common between all pLabs.
pLabs will receive frozen samples in dry-ice (feces and/or soil) to be treated according to the 3 different methods in duplicate. Each pLabs will then send treated (stabilized) samples to 2 designed MS lab (one set of 3 samples each).
pLabs will receive any special reagent required for the 2 - additional - common methods MS analyses will be provided by the organizers as a collaborative service. CAMPI 2 does not focus on comparative analysis of MS performances on a standard sample. A further CAMPI dedicated to these issues will be organized in the next future.
Metagenomic analysis of the soil and fecal bulk samples will be provided by the organizers to generate DBs.
pLabs are required to cover the costs for the fecal and/or the soils samples pick up and delivery from/to their lab.
The MS labs will extract the peptides with a standardized protocol and acquire MS/MS data to obtain comparable datasets. The MS data will be analyzed all together by one bioinformatic group. All resulting data will be shared with all participants and discussed together. CAMPI 2 results will be composed in at least one collaborative scientific manuscript involving all participants. Online meetings will be scheduled before the shipment of samples to pLabs and at defined time points according to program progression.
This call will close on January 12, 2023 at 5pm CET
Application must be sent by email CAMPI2MPI@gmail.com using the CAMPI 2 application form.
Further details and any sort of questions can be addresses to: Sergio Uzzau - firstname.lastname@example.org.
Selection of pLabs
Based on sample amounts constraints and on the focus of this study, the collaborative tasks will be developed with the participation of no more than 10 laboratories for soil and no more than 10 for fecal samples. Therefore, maybe not every application can be considered. CAMPI 2 participants will be selected according to the following main criteria :
- Geographic area (aiming to have involved labs in the highest possible number of different geographic areas; this will enable to test long distance and diverse logistics in sample shipment from pLabs to MS “central” laboratories).
- Research experiences as declared in application forms
- Variety of suggested sample stabilization methods