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CHANDRAN V R"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Planktonic","Lc-ms/ms","Biofilm","Enterococcus faecalis sk460"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD010770"],"sample_protocol":["The strain Enterococcus faecalis SK460 is a strong biofilm former and was isolated from chronic diabetic foot infection. The strain was cultured in planktonic (12hr, 24hr) and biofilm stages (12hr, 24hr) for protein isolation to carry out quantitative proteome analysis. The cell pellet obtained from different planktonic and biofilm stages were resuspended in PBS (1ml PBS per gram of cells) and transferred to 2ml microcentrifuge tubes containing glass beads (0.5mm), Protease inhibitor (1mM PMSF) and incubated on ice for 5 minutes. The tubes were then placed in a Mini Bead beater (BioSpec Products, USA) and subjected to three, one minute pulses at 4200 rpm with 1 min interval. The suspensions were centrifuged for 10 min at 13,000 rpm at 4 °C and the supernatant was collected. Protein concentration was estimated by bicinchoninic acid protein assay kit (Thermo Scientific, USA). 100 micrograms of protein from each sample were used for in-solution trypsin digestion. DL-dithiothreitol (10 mM) (Sigma-Aldrich, USA) in 50mM ammonium bicarbonate (Sigma-Aldrich, USA) buffer at 60ᴼC for 30 minutes was used to reduce the disulfide bonds. The subsequent alkylation of proteins was done with 200mM iodoacetamide (Sigma-Aldrich, USA) in the same buffer at 27°C for 30 minutes in the dark. The alkylated proteins were digested with trypsin (sequencing-grade modified trypsin, Sigma-Aldrich, USA; 1:25 w/w) in 50mM ammonium bicarbonate buffer by incubating overnight at 37ᴼC. Formic acid(Sigma-Aldrich, USA; 1% v/v) was used to terminate the trypsin digestion reaction. The digested peptide solution was centrifuged at 14,000 rpm at 4ºC for 12 minutes, and the supernatant was stored at -20ᴼC until the LC/MS/MS analysis. The peptide samples were analyzed by using a nano ACQUITY UPLC® System (Waters, UK) coupled to a Quadrupole-Time of Flight (Q/TOF) mass spectrometer (SYNAPT-G2, Waters, UK) controlled by MassLynx4.1 SCN781 software (Waters, UK). In each sample, equivalent to 3µg of protein (3µl), was injected in ‘partial loop’ mode and was loaded into the reverse phase column with 0.1% formic acid in water as mobile phase A, and 0.1% formic acid in acetonitrile as mobile phase B, using the binary solvent manager. The trap column (Symmetry® 180µm x 20mm C18 5µm, Waters, UK) was used to remove any salt by employing a high flow rate (15µl/minute) with 99.9% mobile phase A and 0.1% mobile phase B for 1 minute. The peptide separation was performed in a 75µm x 100mm BEH C18 column (Waters, UK), with a particle size of 1.7µm. Gradient elution with 1-40% mobile phase B, for 55.5 minutes at 300nl/minute flow rate, was employed. After separation, the column was washed with 80 % mobile phase B for 7.5 minutes and re-equilibrated with 1% mobile phase B for 20 minutes. The column temperature was maintained at 40ᴼC. Three technical replicate runs were performed for each sample. Peptides eluted from the nano-LC were monitored by SYNAPT® G2 High Definition MS™ System (HDMSE System (Waters, UK). The time of flight analyzer (TOF) was calibrated with a solution of 500fmole/µl of human [Glu1]-Fibrinopeptide B (Sigma Aldrich, USA), and the lock mass acquisition was performed every 30 seconds by the same peptide delivered through the reference sprayer of the nano-LockSpray source at a flow rate of 500nl/minute. This calibration sets the analyzer to detect ions in the range of 50 - 2,000 m/z. The mass spectrometer was operated in the ‘resolution mode’ with a resolving power of 18,000 FWHM, and the data acquisition was performed in ‘continuum’ format. The data were acquired by rapidly alternating between two functions – Function-1 (low energy) and Function-2 (high energy-MSE). Each spectrum was acquired in 0.9 seconds with an interscan delay of 0.024s."],"repository":["Pride"],"quantification_method":["Spectrum counting","Peptide counting"],"modification":["Carbamidomethyl","Oxidation"],"data_protocol":["The acquired ion mobility enhanced MSE spectra was analysed using ProteinLynx Global SERVER™ v3.0.2 (PLGS, Waters) for protein identification as well as for the label-free relative protein quantification. Data processing includes lock mass correction post acquisition. Processing parameters for PLGS were set as follows: noise reduction thresholds for low energy scan ion – 150 counts, high energy scan ion - 50 counts and peptide intensity - 500 counts (as suggested by manufacturer). The protein identifications were obtained by searching against Enterococcus faecalis V583 (NCBI Reference Sequence: NC_004668.1). During database search, the protein false positive rate was set to 1%. The parameters for protein identification was made in such a way that a peptide was required to have at least 1 fragment ion match, a protein was required to have at least 3 fragment ion matches and a protein was required to have at least 1 peptide match for identification. Oxidation of methionine was selected as variable modification and cysteine carbamidomethylation was selected as a fixed modification. Trypsin was chosen as the enzyme used with a specificity of 1 missed cleavage. Data sets were normalized using the ‘auto-normalization' function of PLGS and label-free quantitative analyses was performed by comparing the normalized peak area/intensity of identified peptides between the samples. Furthermore, only a fold change higher than 50% difference (ratio of either <0.50 or >2) was considered to be indicative of significantly altered levels of expression."],"omics_type":["Proteomics"],"labhead":["Dr.Sabu Thomas"],"instrument_platform":["Synapt MS"],"labhead_affiliation":["scientist EII , Rajiv Gandhi centre for Biotechnology"],"submission_type":["COMPLETE"],"species":["Enterococcus Faecalis (streptococcus Faecalis)"],"submitter_mail":["maheshchandran@rgcb.res.in"],"publication":["31253082 Suryaletha K, Narendrakumar L, John J, Radhakrishnan MP, George S, Thomas S. Decoding the proteomic changes involved in the biofilm formation of Enterococcus faecalis SK460 to elucidate potential biofilm determinants. BMC Microbiol. 2019 19(1):146 10.1186/s12866-019-1527-2"],"curator_keywords":["Biological"],"submitter_affiliation":["Technician, Mass spectrometry and proteomics core facility, RGCB"],"submitter_country":["India"],"doi":["10.6019/PXD010770"],"pubmed_abstract":["