交联质谱（XL-MS 或 CLMS）

交联质谱（XL-MS 或 CLMS）是一种强大的技术，用于研究蛋白质-蛋白质相互作用、蛋白质复合物结构和蛋白质构象变化。该方法包括使用化学交联剂将蛋白质或蛋白质之间相互作用或紧密位于的氨基酸共价连接。然后将交联蛋白质消化成肽，通过质谱分析交联肽。

交联质谱的一般工作流程如下：

1. 交联：将蛋白质或蛋白质复合物与化学交联剂处理，使其在近距离的氨基酸之间形成共价连接。交联剂的选择取决于实验要求，例如所需的交联距离和用于交联的特定氨基酸。

2. 消化：将交联蛋白质消化成肽，使用蛋白酶如胰蛋白酶，它在特定的氨基酸序列处切割蛋白质。

3. 富集：根据使用的交联剂和实验设计，可能需要从复杂的肽混合物中富集交联肽。这可以通过多种方法实现，包括亲和纯化、大小排阻层析或强阳离子交换层析。

4. 质谱分析：使用高分辨率质谱对交联肽进行分析。质谱仪测量肽的质量与电荷比（m/z），提供关于其质量和电荷的信息。串联质谱（MS/MS）用于将交联肽片段化并获得其序列信息。

5. 数据分析：使用专门的生物信息学工具和算法分析结果的质谱数据。这些工具有助于识别交联肽并推断相互作用的氨基酸或蛋白质区域。所识别的交联可用于生成结构模型或绘制蛋白质相互作用界面。

交联质谱已成功应用于研究各种生物系统，包括蛋白质-蛋白质相互作用、蛋白质-核酸相互作用和蛋白质-脂质相互作用。它还被用于研究大型蛋白质复合物和膜蛋白的结构和动态。

Crosslinking mass spectrometry (XL-MS or CLMS) is a powerful technique used to study protein-protein interactions, protein complex structures, and protein conformational changes. The method involves covalently linking interacting or closely located amino acids within a protein or between proteins using chemical crosslinkers. The crosslinked proteins are then digested into peptides, and the crosslinked peptides are analyzed using mass spectrometry.

The general workflow of crosslinking mass spectrometry is as follows:

1. Crosslinking: Proteins or protein complexes are treated with a chemical crosslinker that covalently links amino acids in close proximity. The choice of crosslinker depends on the experimental requirements, such as the desired crosslinking distance and the specific amino acids targeted for crosslinking.

2. Digestion: Crosslinked proteins are digested into peptides using proteolytic enzymes such as trypsin, which cleaves proteins at specific amino acid sequences.

3. Enrichment: Depending on the crosslinker used and the experimental design, it may be necessary to enrich crosslinked peptides from the complex peptide mixture. This can be achieved using various approaches, including affinity purification, size-exclusion chromatography, or strong cation exchange chromatography.

4. Mass spectrometry analysis: The crosslinked peptides are analyzed using high-resolution mass spectrometry. The mass spectrometer measures the mass-to-charge ratios (m/z) of the peptides, providing information about their mass and charge. Tandem mass spectrometry (MS/MS) is used to fragment the crosslinked peptides and obtain their sequence information.

5. Data analysis: The resulting mass spectrometry data are analyzed using specialized bioinformatics tools and algorithms. These tools help identify the crosslinked peptides and infer the interacting amino acids or protein regions. The identified crosslinks can be used to generate structural models or map protein interaction interfaces.

Crosslinking mass spectrometry has been successfully applied to study various biological systems, including protein-protein interactions, protein-nucleic acid interactions, and protein-lipid interactions. It has also been used to investigate the structure and dynamics of large protein complexes and membrane proteins.

Crosslinking mass spectrometry (XL-MS) has been under development since the late 1990s and early 2000s. Early work in the field focused on optimizing the crosslinking and mass spectrometry techniques, as well as developing computational methods to analyze the resulting data. The technique has evolved significantly over the past two decades, thanks to advancements in mass spectrometry instrumentation, crosslinking reagents, and bioinformatics tools.

One of the pioneering studies in XL-MS was published in 2000 by Rappsilber, Siniossoglou, et al., who used the technique to study the structure of protein complexes in yeast cells. Since then, numerous improvements have been made to the method, leading to its widespread adoption in the field of structural biology and proteomics.

As the technology continues to mature, XL-MS has become an essential tool for studying protein-protein interactions, protein complex structures, and protein conformational changes, providing valuable insights into the molecular mechanisms underlying various biological processes.

Fan Liu's lab, based at the Max Planck Institute of Biochemistry in Germany, has made significant contributions to the field of crosslinking mass spectrometry (XL-MS). The group focuses on developing innovative XL-MS methods, as well as computational tools for data analysis, to study protein structures and interactions.

One of the key contributions from the Fan Liu lab is the development of the xQuest/xProphet software suite. xQuest is an algorithm for identifying crosslinked peptides from mass spectrometry data, while xProphet is a post-processing tool that statistically validates the xQuest results. This software suite has greatly facilitated the analysis of XL-MS data and is widely used in the field.

The lab has also contributed to the development of novel crosslinking reagents and methodologies for studying protein interactions. For example, they have developed a method called "disuccinimidyl sulfoxide (DSSO) crosslinking" that enables the identification of interacting protein regions by using a photoactivatable crosslinker.

Furthermore, Fan Liu's group has applied their XL-MS expertise to investigate the structure and function of various biologically significant protein complexes, such as the 26S proteasome, the Mediator complex, and the nuclear pore complex, providing valuable insights into the molecular mechanisms of these systems.

Overall, the Fan Liu lab has played an important role in advancing the field of crosslinking mass spectrometry and continues to push the boundaries of what can be achieved with this powerful technique.

二琥珀酰亚砜基 (disuccinimidyl sulfoxide) 交联是一种在蛋白质结构和相互作用研究领域中使用的交联方法。通过使用这种光活化交联剂，可以识别相互作用的蛋白质区域。在交联质谱（XL-MS）技术中，二琥珀酰亚砜基 (DSSO) 交联为研究蛋白质复合物结构提供了一种有效的工具。

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