Protein Fractionation and Enrichment Prior to Proteomics Sample Preparation. In: Mirzaei H, Carrasco M, editors. Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Cham: Springer International Publishing; 2016. pp. 23-41. [DOI: 10.1007/978-3-319-41448-5_2]

Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics

Differential precipitation of proteins (DiffPOP) is a simple technique for fractionating complex protein mixtures. Using stepwise addition of acidified methanol, ten distinct subsets of proteins can be selectively precipitated by centrifugation and identified by mass spectrometry-based proteomics. We have previously shown that the ability of a protein to resist precipitation can be altered by drug binding, which enabled us to identify a novel drug-target interaction. Here, we show that the addition of DiffPOP to a standard LC-MS proteomics workflow results in a three-dimensional separation of peptides that increases protein coverage and peptide identifications. Importantly, DiffPOP reveals solubility differences between proteoforms, potentially providing valuable insights that are typically lost in bottom-up proteomics.

A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry

Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.

Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform Characterization

Top-down mass spectrometry (MS)-based analysis of larger proteoforms (>50 kDa) is typically challenging due to an exponential decay in the signal-to-noise ratio with increasing protein molecular weight (MW) and coelution with low-MW proteoforms. Size exclusion chromatography (SEC) fractionates proteins based on their size, separating larger proteoforms from those of smaller size in the proteome. In this protocol, we initially describe the use of SEC to fractionate high-MW proteoforms from low-MW proteoforms. Subsequently, the SEC fractions containing the proteoforms of interest are subjected to reverse-phase liquid chromatography (RPLC) coupled online with high-resolution MS. Finally, proteoforms are characterized using MASH Explorer, a user-friendly software environment for in-depth proteoform characterization.

A new strategy of studying protein-protein interactions: Integrated strong anion exchange/reversed-phase chromatography/immunoprecipitation coupled with mass spectrometry for large-scale identification of proteins interact with immunoglobulin G in HeLa cells

Recently, significant research efforts have been devoted to the development of technology for large-scale analysis of protein-protein interactions. Herein, a comprehensive method by coupling the first-dimension strong anion exchange chromatography with the second-dimension reversed-phase liquid chromatography via immunoprecipitation technique and high-resolution mass spectrometry analysis was developed for analyzing protein-protein interactions. After two-dimensional liquid chromatography separation, 108 fractions were obtained in one experiment. Immunoglobulin G from human serum was used as a model of an interacting protein. As a result, 919 proteins in these fractions were identified to interact with immunoglobulin G. By searching STRING database and data analysis, 27 of 919 proteins were inferred to directly interact with immunoglobulin G. Moreover, important target proteins that interacted with immunoglobulin G were mapped in the two-dimensional liquid chromatography system, which facilitated selection of these proteins from specific fractions. These results demonstrated that the proposed method can be useful for large-scale investigation of protein-protein interactions and as an advanced tool for the isolation of target proteins.

Improving deep proteome and PTMome coverage using tandem HILIC-HPRP peptide fractionation strategy

Despite being orthogonal to reverse-phase separation and valuable for posttranslational modification (PTM) pre-enrichment, hydrophilic interaction liquid chromatography (HILIC) has not been widely adopted for large-scale proteomic applications. Here, we first evaluated the performance of HILIC in comparison with the popular high-pH reverse-phase (HPRP) separation, as the first dimension for tryptic peptide fractionation in a shotgun workflow to characterize the complex 293T cell proteome. The data indicated that the complementary nature of HILIC and HPRP for peptide separation was mainly due to different hydrophobicity preferences. Realizing that uncaptured components from one mode can be resolved in the other mode, we then designed and compared two multidimensional separation schemes using HILIC and HPRP in tandem for peptide prefractionation, in terms of identification efficiency and coverage at peptide, protein, and PTM levels. A total of 22,604 and 23,566 peptides corresponding to 4481 and 4436 proteins from 293T cell lysate were detected using HILIC-HPRP- and HPRP-HILIC-based shotgun proteomics workflow, respectively. In addition, without assistance of enrichment techniques, the tandem fractionation methods aided to identify 46 different PTMs from over 10,000 of spectra using blind modification search algorithm. We concluded that HILIC is a valuable alternative option for peptide prefractionation in a large-scale proteomic study, but can be further augmented with the use of a secondary HPRP separation.