Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075511/Listeria_monocytogenes_Results.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075511/Key.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075511/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075511/Listeriamonocytogenes.7zprimaryOK200pskan@aua.grPanagiotis SkandamisMass SpectrometryData-independent acquisitionBottom-up proteomicsProteomics protein content nanolc-ms/ms bottom-up proteomics bacteria listeria monocytogenes timstof ultra2https://www.ebi.ac.uk/pride/archive/projects/PXD07551130 µl of the protein extract was taken for further analysis. The mixture was subjected to alternating heating and sonication twice. Subsequently, the sample was centrifuged at 17,000 × g for 15 min and the supernatant was treated according to Hughes’ single-pot solid-phase enhanced sample preparation (Sp3) method [6] without acidification and protein alkylation was performed by adding cysteine to 100 mM iodoacetamide. Digestion was performed at 1200 rpm and 37 °C using 0.5 µg trypsin-platinum mixture in 100 mM TEAB buffer. The next day, magnetic particles were removed, and the peptide sample was further purified using the Sp3 peptide purification kit as previously described [6]. Briefly, 30 μl of the peptide mixture was added to 1.2 ml of acetonitrile (ACN) and they were mixed by inversion for 30 minutes, then the tubes were placed on a magnetic rack. The supernatant was removed and the remaining sample was washed twice with 200 µl of 100% ACN, removing the bound peptide magnetic particles with each wash. Subsequently, 50 µl of water was added to elute the peptide and magnetic particles. The elution buffer was concentrated using SpeedVac. Finally, the dried peptide was dissolved in buffer A, sonicated for 5 minutes, and the absorbance was measured at 280 nm using a Nanodrop spectrophotometer to determine the peptide concentration. 1-D nanoLC-MS/MS analysis The peptide content of the samples was then analyzed using a NanoElute 2 liquid chromatography system coupled to a timsTOF Ultra2 mass spectrometer (Bruker Daltonik GmbH). Briefly, peptides were separated on a temperature-controlled (50 °C) Pepsep column (25 cm × 75 µm, 1.9 µm particle size, Bruker) and ionized using a Captive Spray Ultra-2 ion source. Peptide elution from the column was performed using a 30-minute gradient elution. The mass spectrometer was in dia-PASEF mode, using standard methods for small sample volumes (mobilities 0.64–1.45, cycle time 0.96 s). Complete MS data were acquired in the range of 400–1000 m/z. The ion mobility settings included three isolation windows, all of which were covered in a single TIMS scan. Eight TIMS scans were required to cover all 24 windows.PrideThe timsTOF raw data was analysed in Proteoscape environment using the Spectronaut software version 19, searching against the reference Listeria monocytogenes database retrieved from Uniprot in the library free mode of the software, allowing up to two tryptic missed cleavages. Default settings have been used with oxidation of methionine residues and acetylation of the protein N-termini set as variable modifications and carbamidomethylation of cysteine residues as fixed modification. N-terminal methionine excision was also enabled. The match between runs (MBR) feature was used for all analyses and the output (precursor and protein group) was filtered at 1% FDR.ProteomicsDr. Panagiotis SkandamisPARTIALLaboratory of Food Quality and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 118 55 Athens GreeceListeria Monocytogenes Egd-eNot availablepskan@aua.grAgricultural University of AthensGreecefalseProteomic data of Listeria monocytogenesListeria monocytogenes is an important food-borne pathogen that is responsible for contamination of a variety of food products. It causes listeriosis which is one of the most severe and serious diseases whose symptoms might include nausea and diarrhea. Also because of its ability to adhere to industrials’ surfaces, it is difficult for them to come up against this danger. Although there are researches in L. monocytogenes proteome, most of them are based on the study of a single strain, yet little is known about the proteome of more of the microbe’s strains. By studying the proteome of the microorganism with state-of-the-art mass spectrometry technology in terms of proteomics, we will be able to have an overall picture of the pathogenicity of the bacterium, as this is largely based on its ability to adapt to certain environments and to project its toxicity in them. To address that we provide a dataset of 2227 different proteins from 4 strains of L. monocytogenes, grouped by their molecular function and their biological process. The identified proteins confirm the complex molecular mechanisms of the bacterium.2026-04-072026-03-11PXD075511NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:373995NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:4113NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:145943NEWT:3635NEWT:5811NEWT:1480154NEWT:235443NEWT:1274414NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:70910000-0001-7878-5897