Metaproteomics samples were collected by McLane pump onto 0.2 micron Supor membrane filters, with 51 and 3.0 micron prefilters. Global metaproteomic analyses were conducted using 1-dimensional (1D) and 2-dimensional (2D) chromatographic separation for the Metzyme and ProteOMZ expeditions respectively. Following global metaproteomic analyses, targeted metaproteomic assays were designed and samples were analyzed again by parallel reaction monitoring (PRM) mass spectrometry using mass spectral information from the global proteomic analyses. See methods in Saito et al., 2020 Nature Geosciences for full details.

Samples were analyzed on a Thermo Fusion Orbitrap mass spectrometer. See methods in Saito et al., 2020 Nature Geosciences for full details.

Data quality flags are included following GEOTRACES conventions for results below detection limit (flag= 6). 

Parameters were named using the prior GEOTRACES IDP parameter naming convention used for peptides (PEP), although these are new parameters not previously submitted here or elsewhere.

The peptide parameter naming convention was developed in collaboration with the GEOTRACES program. In other to avoid the sustainability challenge of having to maintain a parameter key of codes that represent protein and peptide sequences, the tryptic peptide amino acid sequences are inserted into the parameter name, with prefixes and suffixes for additional metadata. For example, the parameter name "PEP_MTIQWGK_NxrA_PUMP" has the following components. The prefix PEP refers to the peptides datatype, "MTIQWGK" refers to the specific amino acid sequence of the measured peptide, using the IUPAC-IUB 1 letter amino acid naming convention. This sequence can be used to calculate the molecular weight and elemental formula of the molecule that was measured (e.g. see https://web.expasy.org/compute_pi/ and https://web.expasy.org/protparam/). "NxrA" refers to the protein name, in this case nitrite oxidoreductase subunit A. "PUMP" refers to the samping methodology, in order to differentiate when samples may be collected from the same location and depth but by different methods. This approach is useful as tryptic peptides are short enough in sequence to allow their use within parameter names, and each parameter name uniquely describes the molecule being measured, even when, as in this Nxr study, many different peptides are being measured from within a single protein.
Reference: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1984.tb07877.x