Ramírez Carolina Rojas, Yu Fengchao, Polasky Daniel A, Nesvizhskii Alexey I
Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
bioRxiv. 2025 Jul 31:2025.07.28.667198. doi: 10.1101/2025.07.28.667198.
Conventional database search methods for proteomics struggle when tasked to identify dozens or hundreds of modifications simultaneously. Open or error-tolerant searches can address this limitation, but at the cost of increased difficulty in downstream interpretation of the results and quantification. We and others have previously described "mass offset" or multi-notch searches that sit in between closed and open searches, allowing simultaneous search for hundreds of modifications with more straightforward downstream interpretation than open search. The original mass offset searches were closer to open search, lacking the ability to restrict modifications to specific amino acids. Here, we describe a new "detailed" mass offset (DMO) search implemented in the MSFragger search engine, which allows each mass offset to have its own site restrictions and fragmentation rules. The benefits of DMO search over existing mass offset searches are shown with three example searches of complex modification sets: nearly one hundred post-translational modifications, fast photochemical oxidation of proteins (FPOP)-derived modifications, and amino acid substitutions. The DMO search further improves the interpretability of results by reducing ambiguity in site localization, particularly when modifications have overlapping masses, and provides benefits that scale with the complexity of the search.
蛋白质组学的传统数据库搜索方法在需要同时识别数十种或数百种修饰时会遇到困难。开放搜索或容错搜索可以解决这一局限性，但代价是结果的下游解释和定量难度增加。我们和其他人之前描述过“质量偏移”或多缺口搜索，它介于封闭搜索和开放搜索之间，允许同时搜索数百种修饰，并且下游解释比开放搜索更直接。最初的质量偏移搜索更接近开放搜索，缺乏将修饰限制在特定氨基酸的能力。在这里，我们描述了一种在MSFragger搜索引擎中实现的新的“详细”质量偏移（DMO）搜索，它允许每个质量偏移都有自己的位点限制和碎裂规则。通过对复杂修饰集的三个示例搜索展示了DMO搜索相对于现有质量偏移搜索的优势：近一百种翻译后修饰、蛋白质的快速光化学氧化（FPOP）衍生修饰和氨基酸替换。DMO搜索通过减少位点定位的模糊性进一步提高了结果的可解释性，特别是当修饰具有重叠质量时，并且提供了与搜索复杂性成比例的优势。
