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SinghData-dependent acquisitionMass SpectrometryAdp-ribosylationProteomicsEthcdHcdMacrophagehttps://www.ebi.ac.uk/pride/archive/projects/PXD067389Cell CultureMacrophageTHP-1-derived macrophages (THP-1-Mφ, 2 X 15 cm dishes pooled per treatment and replicate) were treated with phosphate buffered saline (PBS, VWR International, Cat# 12001-680) alone as a control or 10 ng/mL IFN-γ (R&D Systems, Cat# 285-IF) in PBS, with n=5 replicates per condition . After 6 hours, the cells were washed twice with ice-cold PBS, and then the cells were lysed in modified RIPA buffer (50 mM Tris-HCl pH 7.4, 0.4 M NaCl [Sigma-Aldrich, Cat# S9888], 1.0 mM EDTA [Boston Bio Products, Cat# BM-150], 1.0% nonidet P-40 [Sigma-Aldrich, Cat# 74385], 0.1% sodium deoxycholate [Sigma-Aldrich, Cat# D6750], 40 μM PJ34 [Abcam, Cat# ab120981], 1.0 μM ADP-HPD [Millipore Sigma, Cat# 118415], protease inhibitor cocktail [Sigma-Aldrich, Cat# P8340]). THP-1-Mφ lysates were homogenized on ice using sonication. Homogenized lysates were precipitated in acetone (Fisher Scientific, Cat# A949-1). The cell pellets were resuspended in a denaturation buffer (6.0 M urea [Sigma-Aldrich, Cat# U4884], 2.0 M thiourea [Sigma-Aldrich, Cat# T7875], 10 mM HEPES [Boston BioProducts, Cat# BBH-80]). The protein amount was determined by a Pierce 660 nm Protein Assay Reagent (Thermo Fischer Scientific, Cat# 22660). Proteins (5.0–10 mg) were reduced in 1.0 mM dithiothreitol (DTT, Thermo Fisher Scientific, Cat# 20290) and alkylated in 5.5 mM chloroacetamide (Sigma-Aldrich, Cat# C0267). Proteolysis was performed with trypsin (Thermo Fisher Scientific, Cat# 90058) in 20 mM ammonium bicarbonate (Sigma-Aldrich, Cat# 09830) overnight. The peptides were desalted using Sep-Pak C18 Classic Cartridge (Waters, Cat# WAT051910) by following the manufacturer's instructions. Using a Concentrator plus complete system (Eppendorf AG), the peptide sample was reduced to a final volume of 0.8 mL of affinity precipitation buffer (50 mM Tris-HCl pH 7.4, 10 mM MgCl2 [Thermo Fisher Scientific, Cat# AM9530G], 250 μM DTT, 50 mM NaCl). The peptide amount was determined by using a NanoDrop One Spectrophotometer at 205 nm (ε205=31 methods, Thermo Fisher Scientific). The peptides (2-4 mg) were treated with PARG overnight (1.0 μg PARG per 1.0 mg peptide, Creative BioMart, Cat# PARG-31H) to obtain only MARylated peptides. ADPr (MARylated) peptides were enriched using the Archaeoglobus fulgidus ribosylation binding protein eAf1521 macrodomain affinity pull-down as described previously (3, 7, 12). The peptides were then processed using the Microcon-30 kDa Centrifugal Filter Unit (Millipore Sigma, Cat# MRCF0R03) and desalted using Oasis HLB cartridge (30 mg [Waters, 1 cc, Cat# WAT094225]) as per manufacturer’s instructions. The peptides were suspended in loading buffer (5.0% acetonitrile [Fisher Scientific, Cat# A955-1], 0.5% formic acid [Thermo Fisher Scientific, Cat# 28905] in water [Fisher Scientific, Cat# W6-1]) for mass spectrometric analysis.PrideNot availableThe Orbitrap Fusion Lumos was fronted with a FAIMS Pro and EASY-Spray Source, coupled to an Easy-nLC1200 HPLC pump (Thermo Fisher Scientific). The peptides were fractionated using a dual column set-up: an Acclaim™ PepMap™ 100 C18 HPLC Columns, 75 µm X 20 mm (Thermo Fisher Scientific, Cat# 164946); and an EASY-Spray™ PepMap™ Neo UHPLC Column, 75 µm X 150 mm (Thermo Fisher Scientific, Cat# ES75150PN). Binary mobile phases (A: water/0.1% formic acid; B: 95% acetonitrile/5% water/0.1% formic acid) were employed at the flow rate of 300 nL/min. The analytical gradient was from 5% to 21% B for 60 minutes, followed by ten minutes of 21% to 30% B, and a 15-minute column wash alternating between 95% B and 5% B, held for 3 minutes each, in between a 2-minute ramp up or down. Post the washes, the column was equilibrated at 95% B. The mass spectrometers were operated in positive mode. HCD properties of ADPr peptides. The MS1 resolution was set to 120,000 with a scan range of m/z 400-900. Ions with a charge state of 2-6 were selected for MS2 fragmentation, dynamic exclusion was 60 seconds, and intensity threshold was set to 25,000. The total cycle time of the data dependent mode was set to 3 seconds. The MS2 resolution was set to 120,000, isolation window was 1.2 m/z, maximum injection time was dynamic, and collision energy was 28%. EThcD properties of ADPr peptides. The MS1 resolution was set to 120,000 with a scan range of m/z 400-900. Ions with a charge state of 2-6 were selected for MS2 fragmentation, dynamic exclusion was 60 s, and intensity threshold was set to 25,000. The total cycle time of the data dependent mode was set to 3 seconds. The MS2 resolution was set to 120,000, isolation window was 1.2 m/z, maximum injection time was dynamic, and supplemental activation collision energy was 22.5%. Gas-phase segmentation (GPS) is defined as segmenting the MS1 scan range, analysed as separate injections: m/z 400-655 and m/z 645-900. FAIMS was operated on the standard resolution set to static gas mode with a total carrier gas flow of 3.9 L/min. Single compensation voltages (CVs) of -40V, -50V, -60V, -70V, -80V or combined multiple CVs of -60V/-70V/-80V were applied for HCD properties while -40V, -45V, -50V, -55V, -60V, -65V, -70V, -75V, -80V, -85V, or -50V/-60V/-70V were applied for EThcD. ADPr peptide spectra were analyzed using Proteome Discoverer 2.5. The spectra were queried against the Uniprot human fasta database (downloaded January 18, 2022; n=100,730 entries) using the SEQUEST search engine algorithm. Trypsin was set as the digestion enzyme, allowing up to 4 missed cleavages and a minimum peptide length of 6 amino acids. ADPr (+541.061 Da) of Asp, Glu, Lys, Arg, Ser, Thr, Tyr and His; oxidation (+15.995 Da) of methionine; and acetylation (+42.011 Da) of the N-terminus, were set as variable modifications. Carbamidomethylation (+57.021 Da) of cysteine was set as a static modification. Spectral mass tolerances were 10 ppm for the precursor and 20 mmu for the fragment ions. The peptide false discovery rate (FDR) was calculated using Percolator (target/decoy method) and peptide spectrum matches (PSMs) were filtered at 1.0% FDR. ptmRS was used for calculating ADPr site probabilities.ProteomicsMasanori AikawaCenter for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, 02115, United StatesCOMPLETEHomo Sapiens (human)41879802 Kasai T, Weiss L, Wohlfahrt J, Matamalas JT, Shlayen G, Kirsch ZJ, Aikawa M, Aikawa E, Singh SA. Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery. J Proteome Res. 2026 25(4):1941-1950 10.1021/acs.jproteome.5c01012sasingh@bwh.harvard.eduBrigham and Women's Hospital, Harvard Medical SchoolUnited States10.6019/PXD067389Advancements in mass spectrometry and complementary technologies now enable comprehensive, high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease-informative biomarkers. Commercial sources of nondiseased, healthy donor plasma samples are often used for proteomic workflow development and as controls for clinical studies. The overarching assumption is that standard operating procedures for plasma preparation are comparable across different sources. In this study, we investigated the effectiveness of a particle-based protein enrichment strategy against a conventional proteomics workflow on plasma samples from five commonly used commercial sources. We aimed to characterize the extent of variability in plasma proteomes when factors such as freeze-thaw cycles, choice of anticoagulant, and operator-to-operator performance were accounted for in the study setup. Plasma samples were analyzed in data-independent acquisition mode by using two distinct instruments (Exploris 480, timsTOF HT) and search algorithms (CHIMERYS, DIA-NN). Plasma proteome enrichment yields ranged from 2.8- to 6.2-fold more compared to the conventional workflow, achieving yields exceeding 5000 proteins (timsTOF HT). Notably, the observed variability in proteome composition was largely attributable to differences in whole blood-to-plasma operating procedures across commercial sources. While these distinct proteomes remained undetectable with conventional workflows, particle-dependent proteome profiling successfully revealed the procedural differences.Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery.Kasai Taku T, Weiss Luisa L, Wohlfahrt Jessica J, Matamalas Joan T JT, Shlayen Gabriel G, Kirsch Zachary J ZJ, Aikawa Masanori M, Aikawa Elena E, Singh Sasha A SAfalseAn evaluation of high-field asymmetric-waveform ion mobility spectrometry coupled to electron-transfer/higher-energy collision dissociation for ADP-ribosylation proteomicsObjective: ADP-ribosylation is a post-translational modification that plays an important role in cellular processes. Our previous work implemented multiple gas-phase separation strategies (e.g., FAIMS) and in-source CID on the quadrupole-Orbitrap (Exploris 480) to increase the yield and acceptor site confidence scores of HCD-dependent ADP-ribosyl (ADPr) peptide identifications. We evaluated whether FAIMS coupled on the quadruple-ion trap-Orbitrap (Fusion Lumos) also improves EThcD-dependent ADP-ribosyl peptide sequencing. Methods: ADPr peptides derived from the human macrophage-like cell line THP-1 (THP-1-Mφ) were analyzed on the Lumos fronted with a FAIMS Pro and EASY-Spray Source, coupled to an Easy-nLC1200 HPLC pump. Gas-phase segmentation (GPS) for the MS1 scan range, and single and multiple combined compensation voltages (CVs) for FAIMS were applied for HCD and EThcD properties. ADP-ribosyl peptide spectra were analyzed using Proteome Discoverer 2.5. The ptmRS function was used for calculating ADP-ribosyl site probabilities. Results: We evaluated the number of ADPr and non-ADPr PSMs using ADPr peptides pooled from PBS and IFN-γ treated THP-1-Mφ across a range of CVs (-40V to -85V) using FAIMS with HCD and EThcD. The peak CVs for ADPr and non-ADPr PSMs were shifted for HCD, while they represented similar distributions for EThcD. The net number of unique ADPr and non-ADPr peptides across the CVs increased by 3.2- and 3.8-fold more respectively for HCD, and 2.0- and 3.6-fold respectively for EThcD, compared to no FAIMS. We then tested 4 distinct MS methods: (method 1: m/z 400-900, method 2: m/z 400-655 and m/z 650-900, method 3: three CVs combination (-50V, -60V, -70V) with m/z 400-900, method 4: three different acquisitions using distinct CVs (-50V, -60V, -70V) with m/z 400-900) for identifying the maximum number of ADPr acceptor sites with high (>95%) confidence using EThcD. Method 4 was best with 562 ADPr PSMs, but only 54% were high confidence ADPr sites. Due to sample volume limitation, we used method 3 for analyzing ADPr peptides enriched from THP-1-Mφ treated with PBS or IFN-γ separately. We identified 324 and 196 unique ADPr peptides from PBS and IFN-γ, of which 257 and 139 unique acceptor sites were identified with high confidence. The most frequent ADPr acceptor site was lysine (>90%), followed by serine. Conclusion: Our data demonstrated that while FAIMS is valuable for EThcD-dependent sequencing of ADPr peptides, the gains are less for ADPr peptides or contaminant non-ADPr peptides when using HCD.2026-04-132025-08-15PXD067389NEWT:330879NEWT:377960NEWT:1131NEWT:2042546NEWT:259447NEWT:295546NEWT:1334565NEWT:625351NEWT:258594NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:6819NEWT:475174NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:33114NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:3765NEWT:3767NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:1582NEWT:1584NEWT:36630NEWT:383379NEWT:418106NCBITaxon:12721NEWT:10029NEWT:913645NEWT:641809NEWT:1392488NEWT:38815NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:410658NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:1310173NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:150808NEWT:1182590NEWT:3712NEWT:3711NEWT:3714NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:3704NEWT:244366NEWT:1246791NEWT:176597NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1348799NEWT:33995NEWT:55784NEWT:1303443NEWT:485NEWT:56636NEWT:2499525NEWT:2853422NEWT:487NEWT:1538553NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:1502NEWT:128017NEWT:376686NEWT:237610NEWT:95486NEWT:1883446NEWT:1233435NEWT:118223NEWT:11757NEWT:987059NEWT:109760NEWT:29031NEWT:317047NEWT:491NEWT:460523NEWT:45954NEWT:235443NEWT:1757312NEWT:85694NEWT:109786NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:1640278NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:28128NEWT:470NEWT:5911NEWT:748693NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:28141NEWT:9031NEWT:27292NEWT:1050722NEWT:3728NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:207340NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:42410NEWT:36185NEWT:1054211NEWT:1225786NEWT:771870NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:10832NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:1613NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:353153NEWT:227377NEWT:1774284NEWT:40674NEWT:1194669NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:105487NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:28550NEWT:80863NEWT:90675NEWT:52639NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:861109NEWT:8695NEWT:884204NEWT:1045775NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:1028307NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:441772NEWT:1293091NEWT:48106NEWT:202956NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:1076878NEWT:200308NEWT:200302NEWT:870435NEWT:58370NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:2144189NEWT:1392998NEWT:380394NEWT:1150621NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:72664NEWT:563041NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1801631NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:1774208NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:103690NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:285272NEWT:192222NEWT:9963NEWT:1617910NEWT:197911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