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ogy.orgUlrike KusebauchData-dependent acquisitionMass SpectrometryNot availablePlasmaData-dependent acquisitioncat proteomePeptideatlasFeline cell linesTissuesFelis catusFelis catus; cat proteomehttps://www.ebi.ac.uk/pride/archive/projects/PXD075481QuadricepsHeartBrainBlood PlasmaLungLiverCell CultureKidneyCell culture and sample preparation Felis catus G355-5 astrocyte brain cells (ATCC) were cultured in McCoy's 5A Modified Medium with heat-inactivated fetal bovine serum (final concentration of 10%). Felis catus CRFK kidney cells (ATCC) were cultured in Eagle's Minimum Essential Medium with horse serum (final concentration of 10%). Cells were pelleted (1,000 rpm, 15 min, 4°C), pellets were washed with phosphate-buffered saline (PBS, pH 7.4) and stored at -80°C. Frozen pellets were resuspended in 8M urea, 100 mM ammonium bicarbonate with cOmplete protease inhibitor cocktail. Cells were lysed by sonication and lysate centrifuged. The proteome supernatant was collected and quantified (Protein Assay Kit II, Bio-Rad). 100 μg protein from each cell line were reduced with 5 mM Tris (2-carboxyethyl) phosphine hydrochloride (TCEP, 30 min, 80°C), alkylated with 10 mM iodoacetamide (IAM, 30 min, room temperature, darkness), and diluted with 50 mM ammonium bicarbonate to a urea concentration of 1 M. Samples were digested with Trypsin Gold (1:30 trypsin to protein, 16 h, 37° C). The digestion was stopped (0.1 % Trifluoro acidic acid (TFA)). Peptides were cleaned using C-18 Spin Columns per manufacturer’s instruction and dried under centrifugal evaporation. An aliquot of each sample was subjected to high-pH reversed phase peptide fractionation. 32 fractions were combined into eight for LC-MS analysis. In addition, G355-5 cells were lysed and subjected to acetone-precipitation and subjected to digestion. Tissue sample preparation Feline tissues were thawed and rinsed (5x, PBS pH 7.4). 150 mg of each tissue was homogenized in 500 µl 8M urea, 50 mM ammonium bicarbonate buffer with cOmplete protease inhibitor cocktail using a PreCellys Evolution. Protein content was determined (Protein Assay Kit II). An aliquot of 200 μg protein from each tissue was reduced with 5 mM TCEP (15 min, 55 °C), alkylated with 15 mM IAM (30 min, room temperature, darkness, shaking at 800 rpm, Thermomixer), and diluted with 50 mM ammonium bicarbonate to a urea concentration of 1 M. Samples were digested with Trypsin Gold (1:30 trypsin to protein, 16 h, 37° C). The digestion was stopped (0.1 % TFA) and peptides cleaned by using C-18 Spin Columns. Samples were dried under centrifugal evaporation. Plasma sample preparation Plasma was thawed on ice. 100 µL plasma were centrifuged (4000 x g, 10 min) and the pellet of tissue debris discarded. The protein content of the plasma sample was determined by micro bicinchoninic acid assay (BCA). Plasma was subjected to depletion of the 14 most abundant feline plasma orthologue proteins using the human multiple affinity removal system (MARS Hu-14, 4.6 x100 mm, Agilent Technologies) by HPLC according to the manufacturer’s protocol. The depleted fraction was collected in 1.25 mL of MARS Buffer A. The column was regenerated by MARS Buffer B before re-equilibration in MARS Buffer A. The depleted sample was denatured by adding 600 mg urea to 8 M final concentration, reduced with 5 mM dithiothreitol (30 min, 55°C) and alkylated with 14 mM IAM (30 min, room temperature, darkness). The sample was desalted using a HiPrep 26/10 desalting column (Cytiva) with a 1100 HPLC system (Agilent Technologies), and automatically collected in 2 mL of 1% ammonium bicarbonate. The protein concentration of the desalted samples was determined by BCA and samples were digested with 4 µg of Trypsin Gold for 16 h at 37°C. The digested sample was acidified with 5 µL 1% formic acid (FA) and dried under centrifugal vacuum evaporation. Data dependent acquisition (DDA) Peptides were reconstituted in 0.1% FA and analyzed with a high-resolution Q Exactive HF mass spectrometer coupled to an Easy-nLC 1000 system (Thermo Fisher Scientific). Peptides were loaded on an Acclaim PepMap 100 trap (2 cm, 75 μm ID, C18 3 μm) and washed with 0.1% FA in water for 10 min. Peptides were separated on an analytical column (PicoChip, 105 mm, 1.9 um, REPROSIL Pur C-18-AQ, 120Å, New Objective) using 0.1% FA in water (A) and 0.1% FA in acetonitrile (B) (v/v) (Thermo Scientific) with a flow rate of 300 nL/min. A linear gradient from 5% to 35% B in 120 min, followed by 80% B for 5 min and equilibration of the column for 10 min was applied. Further, a linear gradient from 5% to 35% B was applied in 240 min and 480 min followed by equilibration. Survey full-scan MS spectra were acquired in DDA mode in the mass range 375–1375 m/z at 30,000 resolution, automatic gain control (AGC) target set to 1e6 with a 50 ms maximum ion injection time (IT). Peptides were fragmented above a threshold of 2e4 by collision induced dissociation (CID) at a resolution of 15,000, AGC target 1e5, maximum IT50ms, TopN of 40, an isolation width of 1.2 m/z, and a normalized collision energy of 28%. Charge state z = 1, unassigned charges and z ≥ 6 were rejected; dynamic exclusion was set to 60 s. A spray voltage of 1500 V in positive mode and an RF lens at 65% were used.PrideNot availableData Analysis and PeptideAtlas Assembly Q Exactive HF mass spectrometry raw files were converted to mzML format using ProteoWizard msConvert (version 3.0.10505). MS/MS spectra were associated with peptide sequences using Comet (version 2023.01 rev. 2) and MSFagger (version 3.7). The protein search space included (i) the UniProtKB Felis catus proteome (UP000011712, cat, Felis silvestris catus, downloaded October 2023) containing 19,655 entries which represent one protein sequence per gene, (ii) 499 contaminant protein sequences frequently observed in proteome samples (e.g., keratins, trypsin, BSA), and (iii) a sequence-shuffled decoy counterpart. Searched peptides were allowed to be semi-tryptic with up to two missed cleavages. The search parameters included a fixed modification of +57.021464 for carbamidomethylated cysteine and variable modifications of +15.9949 for oxidized methionine and tryptophan, +42.0106 for protein n-terminal acetylation, -17.02650 for pyroglumatic acid formation from glutamine and for cyclization of n-terminal S-carbamoylmethyl-cysteine, -18.01060 for pyroglumatic acid formation from glutamic acid and +0.984016 deamidation of asparagine. A monoisotopic precursor mass error tolerance of 20 ppm was used in Comet and MSFragger with the isotope error setting activated. The search results were processed and statistically validated with the open-source proteomics data analysis package Trans-Proteomic Pipeline (TPP, version v6.4.0 Incus, build 202310260143-9045) including PeptideProphet and iProphet. Peptide spectrum matches (PSM) generated by each search engine were analyzed with PeptideProphet to assign each PSM a probability of being correct. PeptideProphet was run using accurate mass, variable modification count and semi-parametric models. The expectation values were used as the only contributor to the f-value for modeling. The ppm mass errors instead of Daltons were used for mass modeling. Decoy hits were reported with a probability based on the model learned. PeptideProphet results were further processed with iProphet to refine the PSM-level probabilities and compute peptide-level probabilities based on corroborating information from the ensemble of identifications, and to combine the results from the two search engines. All data except plasma were further processed using two rounds of reSpect within the TPP. For the first round of reSpect, the minimum probability was set to 0 and for the second round the minimum probability was set to 0.5. The new set of .mzML files generated by both rounds of reSpect were searched using Comet (version 2023.01 rev. 2) with precursor mass tolerance set to 3.0 and isotope_error off, and processed using PeptideProphet as described above. iProphet was used to process the PeptideProphet validated reSpect results. ProteinProphet was run after iProphet. To assemble a Felis catus PeptideAtlas build from the different experiments, each experiment was thresholded at an iProphet probability that yields a model-based PSM FDR of 0.0001. Decoy identifications were retained and used to compute final decoy-based FDRs. Contaminant protein and peptide identifications were included in the FDR calculation.ProteomicsRobert L. MoritzPARTIALInstitute for Systems Biology, Seattle, WA, USAFelis Catus (cat) (felis Silvestris Catus)ukusebauch@systemsbiology.orgNot availableInstitute for Systems Biology, Seattle, WA, USAUnited StatesfalseDDA data of Felis Catus immortalized cells, tissues and plasmaWe report a mass spectrometry-based proteomics approach to advance the study of the feline proteome. We analyzed immortalized feline cells, various tissues and plasma using data-dependent acquisition (DDA) on a Q Exactive HF mass spectrometer to develop a Felis Catus PeptideAtlas from 157 acquired runs. Data were analyzed using the Trans-Proteomic-Pipeline. We report in the first PeptideAtlas of the domestic cat the identification of 242,844 unique peptides representing 8,972 feline proteins or 45.6% of the predicted UniProtKB Felis catus proteome based on 19,655 unique genes and their representative protein sequences.2026-07-072026-03-11PXD075481NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:376741NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT: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:1283NEWT:931281NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:360094NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091NEWT:5784580000-0001-6162-7577