Table 1.

General recommendations for generating high-confidence proteomic datasets on the human eye.

	Recommendations
Samples	At least three biological replicates
Peptides	≥7 amino acids minimum peptide length Minimum of two peptide match One peptide match if MS2 spectra manually inspected
False discovery rate	Peptide FDR cutoff ≤0.1% Protein FDR cutoff ≤1% Both protein and peptide FDR must be clearly stated in Methods
Protein identifiers	NeXtProt accession should be utilized along with protein name on NeXtProt, with other synonyms removed Peptide sequences used to identify the protein should be included in Supporting Information
Protein isoforms	Manual verification including comparing peptide amino acid sequences compared with sequence alignment of the different isoforms and verification of spectra manually
Missing proteins	Follow HUPO expert committee guidelines[101] Provide MS2 spectra in supplementary material
Mass spectrometry data	MS data should be deposited in ProteomeXchange for inspection and use by the proteomics community