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LenzMass SpectrometrydiaPASEFBottom-up proteomicsAtrial FibrillationCardiacAtrial fibrillationRight ventricleProteomeMass spectrometryhttps://www.ebi.ac.uk/pride/archive/projects/PXD055180HeartPressure cycling tissue lysis and protein digestion Tissue lysis was achieved in a Barocycler 2320XT pressure cycler (Pressure Biosciences, Easton/MA, U.S.A) [Shao et al., 2015]. Samples of approximately 1 mm3 size corresponding to 1-3 mg wet weight were placed into Barocycler micro tubes. 30 µl freshly prepared lysis buffer (Complete protease inhibitor cocktail (Roche, Penzberg, DE), PhosSTOP phosphatase inhibitor cocktail (Roche), 8 M Urea in 100 mM aqueous ammonium biocarbonate pH 8.0) were added and the microtubes centrifuged for 1 min at 5000x G to ensure placement at the bottom. Following 3x10 s sonication to remove air and subsequent centrifugation, microtubes were sealed with micropestles. Tissue lysis was achieved in the Barocycler using 60 pressure cycles consisting of 50 s at 45 kpsi followed by 10 s at normal pressure, respectively. 2 µl aliquots of each sample were removed, diluted 100x and used for protein concentration determination using a microBCA assay on a Nanodrop 2000 UV/Vis Spectrophotometer (Thermo Fisher Scientific, Dreieich, DE). Next, 10 µl 50 mM aqueous TCEP and 10 µl 200 mM iodoacetamide were added to each vial and the samples incubated at for 30 min at 30⁰C in the dark on a thermomixer at 600 rpm to perform reduction and alkylation. Proteolysis was achieved by adding trypsin in 100 mM aqueous ammonium bicarbonate, at a 1:20 enzyme-to-substrate ratio and to a final volume of 150 µl, resulting in a urea concentration of 1.6 M. Microtubes were closed using the appropriate mcirocaps, and again subjected to pressure cycling using 90 cycles consisting of 50 s at 20 kpsi followed by 10 s at normal pressure, respectively at 33⁰C. Following digestion, samples were acidified by adding 12 µl of 10% aqueous trifluoracetic acid, desalted on Pierce C18 spin microcolumns (Thermo Fisher Scientific), taken to dryness in a SpeedVac and stored at -20⁰C until further use. Prior to MS measurement, samples were reconstituted in 20µl of aqueous 0.1% TFA, 2% acetonitrile s containing iRT standard peptides (Biognosys, Schlieren, Switzerland). Mass spectrometry For generation of a peptide library, 150 µg of each cavity-specific pooled protein digest were separated into twenty fractions using a basic pH reversed phase C18 separation on an FPLC system (äkta pure, Cytiva, Marlborough/MA, U.S.A) and a staggered pooling scheme. All samples were spiked with a synthetic peptide standard used for retention time alignment (iRT Standard, Schlieren, Schweiz). Protein digests were analyzed on a nanoflow chromatography system (Dionex Ultimate nanoRSLC, ThermoFisher Scientific) hyphenated to a hybrid timed ion mobility-quadrupole-time of flight mass spectrometer (timsTOF Pro 2, Bruker, Bremen, DE). 400 ng protein equivalent of digested peptides were enriched on a reversed-phase C18 trapping column column (0.3 cm × 300 µm, Thermo Fisher Scientific) and separated on a reversed-phase C18 column with an integrated CaptiveSpray Emitter (Aurora 25 cm × 75 µm, IonOpticks) using a 100 min linear gradient of 5-35 % acetonitrile/0.1% formic acid (v:v) at 250 nl min-1, and a column temperature of 50⁰C. DDA analysis of the fractionated cavity-specific pools was performed in PASEF mode [Meier et al., 2018], with ten scans per topN acquisition cycle. Singly charged precursors were excluded by their position in the m/z–ion mobility plane, and precursors that reached a target value of 20,000 arbitrary units were dynamically excluded for 0.4min. The quadrupole isolation width was set to 2 Th for m/z≤700 and to 3 Th for m/z>700. TIMS elution voltages were calibrated linearly to obtain the reduced ion mobility coefficients (1/K0) using three Agilent ESI-L Tuning Mix ions (m/z 622, 922 and 1,222). Three technical replicates (i.e., MS injection replicates) per C18 fraction were acquired. DIA analysis of individual cardiac biopsies was performed in diaPASEF mode [Meier et al., 2020] using a customized 20x2 variable window size method covering ranges of m/z 350-1350 and 1/K0=0.7-1.5 Vs cm−2, respectively, using the pyDIAid script [Skowronek et al., 2022]. Two technical replicates per sample were acquired.PrideProtein identification, construction of a spectral library and DIA peak integration were achieved in Spectronaut Software v16 (Biognosys, Schlieren, Switzerland) [Bruderer et al., 2015]. Peptides and Proteins were identified using the in-built Pulsar algorithm at default settings. The combined DDA analyses were searched against the UniProtKB Homo sapiens reference proteome (UP000008227, revision 09-2021) augmented with a set of 52 known common laboratory contaminants to identify peptide-to sequence matches, peptides and proteins at false discovery rates (FDR) of 1%, respectively. Peptide identifications were transcribed into an annotated MS/MS spectral library. DIA peak integration was performed using in Spectronaut using manufacturer’s default parameters, with the exception of up the top10 peptides per protein being used for quantitation. Following dynamic retention time correction using endogenous peptides, peak areas were extracted using information from the spectral library at an FDR of 1%. The resulting peak areas were summed to peptide and finally protein area values per replicate, which were statistically evaluated.ProteomicsChristof LenzPARTIALCore Facility Proteomics, Department of Clinical Chemistry, Universitry Medical Center Göttingen, GermanyHomo Sapiens (human)10.1093/CVR/CVAG076christof.lenz@mpibpc.mpg.deMax Planck Institute for Biophysical ChemistryGermanyfalseSpectral library-enhanced label-free proteome profiling highlights the critical role of the right atrium in persistent atrial fibrillationPulmonary veins (PVs) in the left atrium (LA) are a critical site for the initiation of atrial fibrillation (AF). However, the persistent AF (persAF) extends beyond the LA, encompassing both atrial chambers with widespread AF drivers that further promote AF. However, PV ablation remains a cornerstone of AF management. Considering high post-ablation AF recurrence rates in persAF patients, we hypothesized that the right atrium (RA) may play a significant role in the persistence of AF. In this study, we established a comprehensive reference spectral library for the analysis of the human cardiac proteome by data-independent acquisition mass spectrometry (DIA-MS) using material from donor hearts. Application of this library enabled time-efficient and robust analysis of the persAF proteome using RA appendages from patients. Our findings reveal the presence of canonical AF markers and processes within the RA in persAF. Additionally, we observed that the RA mirrors the LA at the proteomic level, losing RA-specific and gaining LA-specific signature proteins in persAF. We conclude that the RA plays a pivotal role in sustaining persAF, underscoring its importance in the clinical management of 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