Assessment of Lactococcus cremoris as an alternative to chemical pre- and post-dipping products

Description

The dataset describes the shotgun proteomics results obtained upon analysis of a Lactococcus cremoris culture used as the basis for a dairy cow teat dip preparation.

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Aliquots of an overnight culture of Lactococcus cremoris were centrifuged for 10 min at 9,300 x g in a refrigerated Eppendorf microcentrifuge. The supernatant was collected and concentrated in Amicon Ultra devices with a molecular cutoff of 10 kDa. Peptides for mass spectrometry analysis were generated from the retentate by on‐filter reduction, alkylation, and trypsin digestion with the filter‐aided sample preparation procedure (Wiśniewski et al., 2009), with minor modifications (Tanca et al., 2014). Shotgun proteomic analysis was carried out by tandem mass spectrometry on a LTQ-Orbitrap Velos (Thermo Fisher Scientific, San Jose, CA, USA) paired with an UltiMate 300 RSLnanoLC system (Thermo Scientific, CA, USA), as described by Pisanu et al., 2015. Briefly, run analysis was performed loading a total of 4 µg of peptide mixture using a linear gradient of 245 minutes. The peptide fraction was concentrated, washed, and separated onto a trapping precolumn (Acclaim PepMap C18, 75 µm × 2 cm nanoViper, 3 µm, 100 Å, Thermo Scientific) and a C18 reverse-phase column (Easy-Spray PepMap C18, 75 µm × 50 cm nanoViper, 100 Å, Thermo Scientific), respectively. Tandem mass spectrometry analysis was performed in a data-dependent MS/MS mode using Higher Energy Collision (HCD) as a fragmentation method and nitrogen as the collision gas. Protein identification was carried out by Proteome Discoverer (version 2.4; Thermo Scientific) as described previously (Addis et al., 2022). Raw files were analyzed against the Lactococcus spp. database (UniptroKb, release_2021_04) and against a custom database generated upon sequencing and annotation of FT72 genome. Gene ontology analysis was carried out with UniProt Knowledgebase (UniProtKB) database to obtain protein annotations for biological processes, molecular functions, and cellular components.Lactococcus spp. database returned 663 protein identifications (sheet A), while the annotated FT27 database returned 16 additional protein identifications (sheet B). All identified proteins were subjected to Gene Ontology for the definition of biological functions (sheet C)

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