Questions before a proteomics enquiry

An enquiry that starts with a method name and a sample count is a form. An enquiry that starts with the contrast, the matrix and the materials you must not ship is a protocol. Write the protocol first. The quote form is where that sheet goes, not where the thinking starts. The method you are specifying is outlined in bottom-up proteomics in plain language. The general habit of a clear sourcing note is how to write a laboratory sourcing enquiry. This page is the proteomics question list itself.

Contrast, matrix and species

Write one sentence the analysis is allowed to answer. "Proteins that differ between drug-treated and vehicle-treated cells of this line, under this exposure" is a sentence. "Full proteome characterisation" is a mood. The sentence decides whether you need identification only, a comparison, or a modification site.

Name the matrix in physical terms. Cultured cells, a dissected tissue, plasma or serum, a gel band, a pull-down eluate, or extracellular medium are different mixtures. Plasma is dominated by a few abundant proteins. A gel band is a small amount of a simpler mixture. A pull-down contains the bait and the bead chemistry. Each one changes cleanup, load and the database contaminants you should expect.

Name the species. Add any engineered sequence: a tagged protein, a fusion, a variant, a codon-optimised recombinant. Those sequences are absent from a species database until someone adds them. Say whether isoforms matter. A study that will claim a splice form needs a database that contains it and a plan to require a unique peptide.

Replicates, amount and chemistry already in the tube

Separate biological replicates from technical ones in the same paragraph. Biological replicates are independent cultures, animals or donors. Technical replicates are repeated digests or repeated injections of one tube. A comparison built only on technical replicates estimates handling noise. It does not estimate biological variation. Write the numbers you have, not the numbers you wish the design had included.

Amount is a class, not a slogan. Say whether you can supply tens of micrograms of protein, or a gel slice whose protein content you have not measured, or a bead eluate in a volume you can name. How laboratories estimate protein concentration is the measurement to do before you ship a figure. If detergent blinds the assay, say which detergent and say the figure is untrusted.

Chemistry already used is the question that prevents a ruined column. SDS, NP-40, Triton, CHAPS, urea, guanidine, glycerol and polyethylene glycol do not all leave the sample by the same cleanup. Write the lysis buffer from the recipe you used, not from memory of a kit name. Protease and phosphatase inhibitors matter when the question involves modifications: a missing inhibitor is a result. A dye or a high salt from an elution is a result too.

Modifications of interest need a direct question. Phosphorylation, acetylation, ubiquitin-like remnants or disulphides each demand different handling and a different search. "Any interesting modifications" is an invitation to a search space that damages the false-discovery rate. Pick the one the biology needs, or say that you want identification with only the routine variable modifications, such as methionine oxidation.

Quantification is a yes or a no. If yes, say whether you need a relative comparison between groups or a more calibrated estimate. If you have no groups, do not ask for fold changes. Acquisition preference is optional. State data-dependent, data-independent or targeted only when you already know why. A targeted enquiry without a peptide list should say that the list does not exist yet.

The database question closes the scientific block. Taxon, reviewed or unreviewed sequences, contaminants, and any custom entry. UniProt is a common source. Name the version if you must match an earlier paper. Otherwise ask for the version to be written into the report so you can match it later.

Decisions the laboratory keeps

Some choices are not a service preference. Whether human samples may be used, whether identifiers have been removed, and whether an infectious agent may leave your building are decisions for your institution. A method reference can discuss a compatible workflow only after those answers are yes or no. Biosafety level is not chosen in a quotation. The WHO Laboratory Biosafety Manual is a public reference for how laboratories think about containment. Your biosafety committee applies the rules you actually work under.

What a discussion can cover is the analytical class: discovery or targeted, identification or a quantitative contrast, routine modifications or an enrichment, and the report fields. What it should not be asked to invent is the biological grouping, the ethics status, or a protein-count promise. protocols.io is where detailed digestion variants are often written. Point at a protocol if you must match one. The Human Proteome Organization is useful background for evidence language, not a substitute for your sample sheet.

Forbidden materials and the temperature on the label

Write a forbidden list: live pathogens you are not cleared to ship, samples with names and hospital numbers still attached, radioisotopes, and volumes of solvent the carrier will not move. Also write the positive list: frozen cell pellets, digested peptides already dried, gel pieces in a stated buffer.

Shipping temperature is part of the chemistry. Peptides and undigested proteins do not tolerate the same handoff. State frozen on dry ice, or cold packs, or ambient for a sample that is genuinely stable, and say which. Storing biological samples from fridge to freezer is the local half of that decision. The enquiry half is what the receiver is allowed to assume when the box arrives.

The report block is the last scientific question. Ask for sample grouping, digestion chemistry, cleanup, acquisition, database version, modifications, false-discovery thresholds, the protein-grouping rule, and, if quantities are claimed, normalisation and the missing-value rule. If you do not ask, you may receive a pathway picture and a spreadsheet of gene symbols.

Biosafety stays with the institution

Repeat the boundary in the sheet itself. "Cleared by our biosafety process for shipment as non-infectious protein" is a statement your institution has to be willing to sign. A quotation cannot create that clearance. Research proteomics remains research. Do not describe the future table as a diagnostic report in the enquiry, or the wrong method will be discussed.

Heat, humidity and the handoff

In hot weather the temperature class on the label is doing chemical work. A pellet that thaws and sits humid can start to degrade and can grow something you did not intend to ship. A peptide tube that warms may oxidise and adsorb. Write the coolant, the backup plan if a courier delays the box, and the name of the person who may open it. If your building loses power often, freeze and pack on a day when the freezer has been cold, and note that history. None of this is a promise about transit time. It is a description of the sample's condition so the receiver does not treat a warm box as a frozen one.

How a quote request should read

Paste the sheet. Include the contrast sentence, the matrix, the species, the replicate counts, the amount class, the buffer recipe, the modification if any, the database needs, the forbidden list, the shipping temperature and the report fields. Ask whether a discovery identification, a quantitative comparison or a targeted follow-up can be discussed for that sheet.

The shotgun discovery proteomics reference, the protein identification by LC-MS/MS reference and the differential abundance reference are the method pages that match those three shapes. Use them as the language of the request. Send the sheet with the quote request. The pages do not mean a study has been opened, and they do not replace the institutional decisions you still have to record.