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McKetneyMass SpectrometryShotgun proteomicsSynaptosomeLc-msmshttps://www.ebi.ac.uk/pride/archive/projects/PXD041108BrainBoth synaptic and whole cell lysate were prepared for mass spectrometry using a modified version of the SPEED method102. Whole cell lysate samples were brought to 80% MeOH before spinning at 16,000 g for 10 minutes. Supernatant was disposed of before pellet was resuspended in a volume of >= 99% TFA, three times that of the pellet. Synaptosome sample pellets were washed twice with PBS before addition of TFA at the same volume proportion. Pellets were allowed to lyse for 5 minutes at room temperature, before acid was quenched with 2M Tris at 10x volume of acid added. Proteins were reduced and alkylated by adding 1.1x acid volume of 100 mM TCEP, 400 mM CAA, bringing the lysates to a final concentration 10mM TCEP and 40 mM CAA, before incubating at 95 C for 5 minutes. Samples were diluted 1:2 with water before protein concentration was determined using the Protein 660 assay (Pierce Thermo Fisher). 70 ug of protein was aliquoted from each sample, and trypsin and lys-C were added, each at a ratio of 1:100 protease to protein. Samples were digested with shaking overnight at 37 C. Digested samples were desalted using a 96-well C18 plate (NEST Group, HNS S18V 20MG PROTO 300 C18), before dried down using a SpeedVac Concentrator. Samples were resuspended in 0.1% formic acid at a concentration of 1 mg/ml before injection onto the LC-MS/MS system. Digested peptides were separated using Thermo EASY-nLC 1200 nano liquid chromatography setup. Synaptosome samples utilized an attached 15 cm long fused silica column filled with 1.7 um bridged ethylene hybrid (BEH) C18 particles. Whole cell samples utilized an attached 25 cm long fused silica column filled with 1.9 um Reprosil-Pur C18 particles. Mobile phase A was composed of a 0.1% formic acid solution, while mobile phase B was composed of 0.1% formic acid with 80% acetonitrile. Sample injections of 1 ul, equating to approximately 1 ug of material, were loaded onto the column at a flow rate of ~ 1 ul/min(maximum pressure of 650 bar). After loading, the gradient began with mobile phase B at 4% for 2 minutes, before increasing to 30% over 60 mins. Mobile phase B then increased to 45% over 10 minutes before increasing to 95% B over 2 minutes and finishing with a wash at 95% B for 6 minutes. The gradient required a total time of 80 minutes. Eluting peptides were ionized by electrospray ionization and analyzed using an Orbitrap Exploris 480 Mass Spectrometer. Four data-dependent acquisition runs were collected for both the whole cell and synaptosome samples, two WT and two heterozygous mutants, to generate a spectral library. Survey scans were taken from 350-1100 m/z at a resolution of 60,000, with a normalized AGC of 300%. Maximum injection time set to “Auto” and Advanced Peak Determination was utilized. Precursors were isolated for tandem MS using a 1.6 m/z isolation window and fragmented using HCD with a normalized collision energy of 30%. Tandem MS scans were taken at a resolution of 15,000 with a normalized AGC of 200% and maximum injection time of 22 ms. Tandem MS scan range was set to “Auto” and isolated precursors were excluded for 45 s with a 10 ppm mass tolerance. Only precursors with a charge state from 2-6 were selected for fragmentation. For data independent acquisition, precursors were isolated for tandem MS using 20 m/z windows with a 2 m/z overlap between windows covering the range of 350-1100 m/z. All other parameters for full scans and tandem MS scans were the same between DDA and DIA runs, with full scans being taken each complete loop of the DIA windows.PrideNot availableSpectral libraries were generated from DDA runs using the MSFragger (MSFragger103, version 3.5), Philosopher104, version 4.4.0), and EasyPQP (version 0.1.30) components inside of the FragPipe graphic user interface. Raw files were searched against a full mouse proteome, downloaded from Uniprot on 12/29/2021. Reversed sequences were appended to the original as decoys and common contaminants were added. For the MSFragger search enzyme specificity was set to trypsin with 2 missed cleavages allowed and precursor and fragment tolerances both set to 20 ppm. Mass calibration and parameter optimization were both used with an isotope error of 0/1/2. Allowable Peptide length was set from 7 to 50 residues and with an acceptable peptide mass range of 500 to 5,000 Da. Carbamidomethylation of cysteine was set as a fixed modification, while methionine oxidation, N-terminal acetylation, pyroglutamate on N-terminal glutamine or cysteine, and pyroglutamate at N-terminal glutamate were all set as variable modifications. The spectral library generated from Fragpipe was used to search DIA files using DIA-NN105.DIA-NN search was run in double-pass mode with match between runs engaged, and protein inference turned off. The quantification strategy was set to robust LC with high precision. Mass accuracy for both full scans and tandem scans was inferred based on the first DIA run of the batch. Search relied only on the spectral library and so no FASTA file was included.ProteomicsNevan J KroganQBI Director and Professor in Cellular and Molecular Pharmacology, UCSFPARTIALMus Musculus (mouse)40054464 Mei Y, Gosztyla ML, Tan X, Dozier LE, Wilkinson B, McKetney J, Lee J, Chen M, Tsai D, Kopalle H, Gritsenko MA, Hartel N, Graham NA, Flores I, Gilmore-Hall SK, Xu S, Marquez CA, Liu SN, Fong D, Chen J, Licon K, Hong D, Wright SN, Kreisberg JF, Nott A, Smith RD, Qian WJ, Swaney DL, Iakoucheva LM, Krogan NJ, Patrick GN, Zhou Y, Feng G, Coba MP, Yeo GW, Ideker T. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. Cell Syst. 2025 16(4):101204 10.1016/j.cels.2025.101204justinmcketney@gmail.comUniversity of California, San FranciscoUnited StatesThe molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the fetal human brain and human induced pluripotent stem cell (hiPSC)-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders-Cullin 3 (CUL3), DEAD-box helicase 3 X-linked (DDX3X), and Y-box binding protein-1 (YBX1)-by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to more comprehensively resolve the synaptic architecture.Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.Mei Yuan Y, Gosztyla Maya L ML, Tan Xinzhu X, Dozier Lara E LE, Wilkinson Brent B, McKetney Justin J, Lee John J, Chen Michael M, Tsai Dorothy D, Kopalle Hema H, Gritsenko Marina A MA, Hartel Nicolas N, Graham Nicholas A NA, Flores Ilse I, Gilmore-Hall Stephen K SK, Xu Shuhao S, Marquez Charlotte A CA, Liu Sophie N SN, Fong Dylan D, Chen Jing J, Licon Kate K, Hong Derek D, Wright Sarah N SN, Kreisberg Jason F JF, Nott Alexi A, Smith Richard D RD, Qian Wei-Jun WJ, Swaney Danielle L DL, Iakoucheva Lilia M LM, Krogan Nevan J NJ, Patrick Gentry N GN, Zhou Yang Y, Feng Guoping G, Coba Marcelo P MP, Yeo Gene W GW, Ideker Trey TfalseGlobal discovery of synapse proteins using multi-omic synaptic signaturesBottom-up proteomics analysis of whole cell lysate and synaptosomes extracted from wild type and Cul3-haploinsufficient mouse 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