Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale

Raw data of nanoLC-IMS-MS/MS (DDA-PASEF) from HeLa whole proteome digest. HeLa cells were lysed in a urea-based lysis buffer (7 M urea, 2 M thiourea, 5 mM dithiothreitol (DTT), 2% (w/v) CHAPS) assisted by sonication for 15 min at 4°C in high potency using a Bioruptor instrument (Diagenode). Proteins were digested with Trypsin using a filter-aided sample preparation (FASP) [Wisniewski <em>et al</em>., 2009] as previously detailed [Distler <em>et al</em>., 2016]. 200 ng of peptide digest were analyzed using a nanoElute UPLC coupled to a TimsTOF PRO MS (Bruker). Peptides injected directly in an Aurora 25 cm x 75 µm ID, 1.6 µm C18 column (Ionopticks) and separated using a 120 min. gradient method at 400 nL/min. Phase A consisted on water with 0.1% formic acid and phase B on acetonitrile with 0.1% formic acid. Sample was injected at 2% B, lineally increasing to 20% B at 90 min., 35% B at 105 min., 95% at 115 min. and hold at 95% until 120 min. before re-equilibrating the column at 2%B. The MS was operated in DDA-PASEF mode [Meier <em>et al</em>., 2018], scanning from 100 to 1700 m/z at the MS dimension and 0.60 to 1.60 1/k0 at the IMS dimension with a 100 ms TIMS ramp. Each 1.17 sec MS cycle comprised one MS1 and 10 MS2 PASEF ramps (frames). The source was operated at 1600 V, with dry gas at 3 L/min and 200°C, without nanoBooster gas. The instrument was operated using Compass Hystar version 5.1 and timsControl version 1.1.15 (Bruker).本数据集为HeLa全蛋白质组酶解物的纳升液相色谱-离子迁移谱-串联质谱（nanoLC-IMS-MS/MS，数据依赖性采集-平行累积连续碎裂，DDA-PASEF）原始数据。实验采用基于尿素的裂解缓冲液（含7 M尿素、2 M硫脲、5 mM二硫苏糖醇（DTT）、2%（w/v）CHAPS），结合4℃下高强度超声处理15分钟（使用Diagenode公司Bioruptor超声仪）裂解HeLa细胞；随后采用滤膜辅助样品制备（filter-aided sample preparation, FASP）方法，以胰蛋白酶对蛋白质进行酶解，具体流程参照已发表的详细步骤[Wisniewski等，2009；Distler等，2016]。取200 ng肽段酶解产物，使用搭载TimsTOF PRO质谱（TimsTOF PRO MS，布鲁克（Bruker）公司）的nanoElute超高效液相色谱（nanoElute UPLC）进行分析；肽段直接上样至Ionopticks公司生产的Aurora系列色谱柱（规格为25 cm × 75 µm内径，1.6 µm C18填料），以400 nL/min的流速采用120分钟梯度洗脱法分离。流动相A为含0.1%甲酸的水溶液，流动相B为含0.1%甲酸的乙腈溶液；样品以2%流动相B的比例进样，梯度线性升高：90分钟时升至20% B，105分钟时升至35% B，115分钟时升至95% B并维持至120分钟，随后以2% B平衡色谱柱。质谱采用数据依赖性采集-平行累积连续碎裂（DDA-PASEF）模式运行[Meier等，2018]，质谱维度扫描范围为100~1700 m/z，离子迁移谱维度扫描范围为0.60~1.60 1/k0，TIMs扫描时长为100 ms；每1.17秒的质谱循环包含1次MS1扫描与10次MS2 PASEF扫描（帧）。离子源电压设置为1600 V，干燥气流速为3 L/min、温度为200℃，未使用nanoBooster气体；仪器操控采用布鲁克公司的Compass Hystar 5.1版本与timsControl 1.1.15版本软件。