Sample Submission Guideline for Metabolomics, Proteomics, Transcriptomics , and Microbiome

Ubiquitination/

Acetylation/
/Succinylation

Technology

Acceptable sample types

Sample requirements

Our proteomics intake

MS-compatibility & handling notes

Recommended controls

IP /

Co-IP/

Pull-down  

Bead–Ab/bait–target complexes (bead pellet)

Requirement: Submit 20 µL bead pellets. Suggestion: Perform IP/PD from ~1×10⁷ cells. After the final wash, rinse beads with PBS or ultrapure water, remove excess liquid, and ship the pellets on dry ice.

On-bead digestion→

LC-MS/MS

Indicate the antibody used (host/isotype/clone) or the pull-down bait format (e.g., tag/ligand).

IP/Co-IP: Isotype IgG, beads-only, Input/Flow-through;

Eluates (acid/peptide/

competitive/

denaturing)

Requirement: Submit ≤ 50 µL eluate containing ~10–20 µg total protein. Suggestion: Use a mild, MS-compatible elution buffer. Do not use Laemmli buffer. If Laemmli was used, run SDS-PAGE and submit excised gel bands instead; ship on dry ice.

Buffer exchange

→digestion

→LC-MS/MS

Specify the elution buffer composition; use low-detergent, MS-compatible buffers. If high SDS is present, we will perform acetone precipitation to exchange buffers (with some protein loss). Acceptable options: mild RIPA buffer or low-pH glycine–HCl.

Pull-down: Bait-only resin, free-ligand competition (peptide/small molecule), mutant bait (interface disruption).

SDS-PAGE

Gel bands (clean excised pieces)

Requirement: Target band(s) clearly visible on the gel. Suggestion: Load ≥ 10 µg/lane for clear bands; provide a gel image with the MW marker and state the protein load per lane. Excise the target band(s), place in low-bind tubes with a few µL ultrapure water, seal, and ship with icepacks. Avoid room-temperature storage.

In-gel digestion →

LC-MS/MS

Prefer Coomassie staining

Submit a blank gel piece from the same gel and/or a neighboring band as background control.

5×10^6 cells or 0.3 g

Sample Class

Sample Type

16S Sequencing

Metagenome Sequencing

Recommended

Minimum

Recommended

Minimum

Solid sample

Feces, Intestinal Contents

2 g

500 mg

200 mg

500 mg

Swab

10 pieces

4 pieces

10 pieces

5 pieces

Tissue

1 g

500 mg

/

/

Water Body Filter Membrane
(pore size 0.22-0.45 μm, diameter 3-4 cm)

2 pieces

1 pieces

3 pieces

1 pieces

Soil, Sludge, Sediment, Humus

3 g

0.5 g

500 mg

200 mg

Liquid sample

Rumen Fluid, Fermentation Broth, Tissue Fluid (with noticeable precipitate after centrifugation)

3 ml,
precipitate 1 g

1 ml,
precipitate 0.5 g

5 ml,
precipitate 300 mg

1 ml,
precipitate 100 mg

Saliva

5 ml

3 ml

5 ml

3 ml

DNA

Concentration ≥5 ng/μl; Total Amount ≥150 ng; Volume ≥ 30 μl; OD260/280 = 1.8-2.0; DNA must have a distinct main band, no degradation, and be free from RNA, proteins, and other impurities. 

Concentration ≥10 ng/μl; Total Amount ≥500 ng; Volume ≥ 50 μl; OD260/280 = 1.8-2.0; DNA must have a distinct main band, no degradation, and be free from RNA, proteins, and other impurities.

Representative Sample

Sampling Method

Serum

Collect whole blood samples using serum separation tubes containing a clot activator. Allow the samples to clot at room temperature for 60 minutes (note: do not shake the tubes). Centrifuge at 3000 rpm for 10 minutes at 4°C, then aliquot 200 μl of the supernatant (serum) into pre-labeled 2 ml centrifuge tubes. Snap freeze the samples in liquid nitrogen for 5-10 minutes, and store them at -80°C.

Plasma

Collect whole blood samples using blood collection tubes containing an anticoagulant (EDTA or heparin sodium). Gently invert the tubes to mix immediately. Centrifuge at 3000 rpm for 10 minutes at 4°C, then aliquot 200 μl of the supernatant (plasma) into pre-labeled 2 ml centrifuge tubes. Snap freeze the samples in liquid nitrogen for 5-10 minutes, and store them at -80°C. (Note: heparin sodium anticoagulant should not be used for microbiome studies.)

Animal Tissues

Euthanize the animal and dissect it using sterile surgical instruments to quickly collect the desired tissue. Rinse the tissue with pre-cooled saline to remove blood, and use forceps to remove connective tissue and hair. Rinse again with pre-cooled saline. Cut the tissue into small pieces using a scalpel or surgical scissors and place them in pre-labeled sterile cryogenic vials. Snap freeze the samples in liquid nitrogen for 5-10 minutes, and store them at -80°C. (For transcriptome studies, rinse with RNase-free water.)

Suspended Cells

Measure the concentration of the cell culture. Transfer a cell suspension containing 1*10^7 cells into a 2 ml centrifuge tube. Centrifuge at 1000g for 10 minutes at 4°C, and discard the supernatant. Quickly wash the cell pellet with pre-cooled PBS (4°C) 2-3 times, each time centrifuging at 1000g for 10 minutes at 4°C and discarding the supernatant. Collect the cell pellet, snap freeze it in liquid nitrogen for 5-10 minutes, and store it at -80°C.

Adherent Cells

Remove the culture medium and quickly wash the cells 2-3 times with pre-cooled PBS solution. Add an appropriate amount of pre-cooled PBS solution to the culture flask and gently scrape the cells off the flask wall into the PBS solution using a cell scraper. Transfer the mixture to an appropriate centrifuge tube and centrifuge at 300g-500g for 5 minutes at 4°C. Discard the supernatant and wash the cell pellet again with pre-cooled PBS solution. Centrifuge at 1000g for 5 minutes at 4°C and discard the supernatant. Resuspend the cell pellet in pre-cooled PBS solution and measure the cell suspension concentration. Transfer a cell suspension containing 10^7 cells into a 2 mL sterile centrifuge tube, centrifuge at 1000g for 10 minutes at 4°C, and discard the supernatant. Collect the cell pellet, snap freeze it in liquid nitrogen for 5-10 minutes, and store it at -80°C.

Microorganisms

Measure the concentration of the microbial culture. Transfer the culture containing the required amount of microorganisms into an appropriate centrifuge tube. Centrifuge at 4000 rpm for 10 minutes at 4°C, and discard the supernatant. Wash the pellet twice with pre-cooled PBS (4°C), each time centrifuging at 1000 rpm for 10 minutes at 4°C and discarding the supernatant. Collect the microbial pellet, snap freeze it in liquid nitrogen for 5-10 minutes, and store it at -80°C. (For bacteria, it is recommended to sample during the logarithmic growth phase.)

Plant Tissues

Collect the desired tissues from at least 3 plants within one biological replicate from the same corresponding positions (e.g., same light exposure direction) and mix them as one sample. For roots, rinse them under running water to remove soil and impurities, wash them 1-2 times with PBS/RNase-free water, and dry the surface with absorbent paper. If the tissues are too large, freeze them in liquid nitrogen and break them into small pieces. Finally, place the samples in suitable centrifuge tubes (10ml/15ml), snap freeze in liquid nitrogen for 5-10 minutes, and store them at -80°C.