Proteomics Network Analysis of Polarized Macrophages

Chakrabarty, Jayanta K.; Kamal, Abu Hena Mostafa; Shahinuzzaman, A. D. A.; Chowdhury, Saiful M.

doi:10.1007/978-1-0716-0802-9_5

Cited by 1 publication

(1 citation statement)

References 18 publications

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“…Although high‐resolution, high mass accuracy systems have been widely used in many AP‐MS studies, low‐resolution instruments are also very capable of handling most AP‐MS applications. Open source proteomics software packages such as Protein Prospector [63] and MaxQuant [64] are also suitable for MS data processing as well as commercial software, such as proteome discoverer from Thermo Scientific [65–67]. The authors concede that while AP‐MS proves to be exceptional for detecting PPIs, however, sometimes it can be ambiguous to distinguish between direct and indirect interactions.…”

Section: Revealing Protein‐protein Interactions Using Affinity Purifimentioning

confidence: 99%

Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks

Zacharias

Fang

Rahman

et al. 2020

J of Separation Science

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Protein post‐translational modifications and protein interactions are the central research areas in mass‐spectrometry‐based proteomics. Protein post‐translational modifications affect protein structures, stabilities, activities, and all cellular processes are achieved by interactions among proteins and protein complexes. With the continuing advancements of mass spectrometry instrumentations of better sensitivity, speed, and performance, selective enrichment of modifications/interactions of interest from complex cellular matrices during the sample preparation has become the overwhelming bottleneck in the proteomics workflow. Therefore, many strategies have been developed to address this issue by targeting specific modifications/interactions based on their physical properties or chemical reactivities, but only a few have been successfully applied for systematic proteome‐wide study. In this review, we summarized the highlights of recent developments in the affinity enrichment methods focusing mainly on low stoichiometric protein lipidations. Besides, to identify potential glyoxal modified arginines, a small part was added for profiling reactive arginine sites using an enrichment reagent. A detailed section was provided for the enrichment of protein interactions by affinity purification and chemical cross‐linking, to shed light on the potentials of different enrichment strategies, along with the unique challenges in investigating individual protein post‐translational modification or protein interaction network.

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Section: Revealing Protein‐protein Interactions Using Affinity Purifimentioning

confidence: 99%