Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics

PrIntMap-R: An Online Application for Intraprotein Intensity and Peptide Visualization from Bottom-Up Proteomics

Bottom-up proteomics (BUP) produces rich data, but visualization and analysis are time-consuming and often require programming skills. Many tools analyze these data at the proteome-level, but fewer options exist for individual proteins. Sequence coverage maps are common, but do not proportion peptide intensity. Abundance-based visualization of sequence coverage facilitates detection of protein isoforms, domains, potential truncation sites, peptide "hot-spots", and localization of post-translational modifications (PTMs). Redundant stacked-sequence coverage is an important tool in designing hydrogen-deuterium exchange (HDX) experiments. Visualization tools often lack graphical and tabular-export of processed data which complicates publication of results. Quantitative peptide abundance across amino acid sequences is an essential and missing tool in proteomics toolkits. Here we created PrIntMap-R, an online application that only requires peptide files from a database search and FASTA protein sequences. PrIntMap-R produces a variety of plots for quantitative visualization of coverage; annotation of specific sequences, PTM's, and comparisons of one or many samples overlaid with calculated fold-change or several intensity metrics. We show use-cases including protein phosphorylation, identification of glycosylation, and the optimization of digestion conditions for HDX experiments. PrIntMap-R is freely available, open source, and can run online with no installation, or locally by downloading source code from GitHub.

A Tyrosine Phosphoproteome Analysis Approach Enabled by Selective Dephosphorylation with Protein Tyrosine Phosphatase

Protein tyrosine phosphorylation (pTyr) plays a prominent role in signal transduction and regulation in all eukaryotic cells. In conventional immunoaffinity purification (IP) methods, phosphotyrosine peptides are isolated from the digest of cellular protein extracts with a phosphotyrosine-specific antibody and are identified by tandem mass spectrometry. However, low sensitivity, poor reproducibility, and high cost are universal concerns for IP approaches. In this study, we presented an antibody-free approach to identify phosphotyrosine peptides by using protein tyrosine phosphatase (PTP). It was found that most of the PTPs including PTP1B, TCPTP, and SHP1 can efficiently and selectively dephosphorylate phosphotyrosine peptides. We then designed a workflow by combining two Ti⁴⁺-IMAC-based phosphopeptide enrichment steps with PTP-catalyzed dephosphorylation for tyrosine phosphoproteomics analysis. This workflow was first validated by selective detection of phosphotyrosine peptides from semicomplex samples and then applied to analyze the tyrosine phosphoproteome of Jurkat T cells. Around 1000 putative former phosphotyrosine peptides were identified from less than 500 μg of cell lysate. The tyrosine phosphosites on the majority of these peptides could be unambiguously determined for over 70% of them possessing only one tyrosine residue. It was also found that the tyrosine sites identified by this method were highly complementary to those identified by the SH2 superbinder-based method. Therefore, the combination of Ti⁴⁺-IMAC enrichment with PTP dephosphorylation provides an alternative and cost-effective approach for tyrosine phosphoproteomics analysis.

Kinase-Catalyzed Biotinylation to Map Cell Signaling Pathways: Application to Epidermal Growth Factor Signaling

Cell signaling involves a network of protein-protein interactions and post-translational modifications that govern cellular responses to environmental cues. To understand and ultimately modulate these signaling pathways to confront disease, the complex web of proteins that becomes phosphorylated after extracellular stimulation has been studied using mass spectrometry-based proteomics methods. To complement prior work and fully characterize all phosphorylated proteins after the stimulation of cell signaling, we developed K-BMAPS (kinase-catalyzed biotinylation to map signaling), which utilizes ATP-biotin as a kinase cosubstrate to biotin label substrates. As a first application of the K-BMAPS method, the well-characterized epidermal growth factor receptor (EGFR) kinase signaling pathway was monitored by treating epidermal growth factor (EGF)-stimulated HeLa lysates with ATP-biotin, followed by streptavidin enrichment and quantitative mass spectrometry analysis. On the basis of the dynamic phosphoproteins identified, a pathway map was developed considering functional categories and known interactors of EGFR. Remarkably, 94% of the K-BMAPS hit proteins were included in the EGFR pathway map. With many proteins involved in transcription, translation, cell adhesion, and GTPase signaling, K-BMAPS identified phosphoproteins were associated with late and continuous signaling events. In summary, the K-BMAPS method is a powerful tool to map the dynamic phosphorylation governing cell signaling pathways.

The challenge of detecting modifications on proteins

Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

Immunoaffinity Targeted Mass Spectrometry Analysis of Human Plasma Samples Reveals an Imbalance of Active and Inactive CXCL10 in Primary Sjögren's Syndrome Disease Patients

One of the most important advantages of mass spectrometry is the ability to quantify proteins and their modifications in parallel to obtain a holistic picture of the protein of interest. Here, we present a hybrid immunoaffinity targeted mass spectrometry (MS) method that combines efficient pan-antibody enrichment of a specific protein from plasma with the selectivity of high-resolution targeted MS analysis to quantitate specific proteoforms of interest. We used this approach to quantify plasma levels of the chemokine CXCL10 that has been associated with many immunological disorders such as systemic lupus erythematosus and primary Sjögren's Syndrome (pSS). The hybrid approach enabled sensitive, specific, and simultaneous quantification of total, full-length (active) CXCL10_1-77 and DPP4-truncated (inactive) CXCL10_3-77 in human plasma down to the low pg/mL level, reaching ELISA sensitivities. Samples from 30 control subjects and 34 pSS patients (n = 64) were analyzed. The ratio of CXCL10_1-77 to truncated CXCL10_3-77 was significantly increased in patients with pSS and provided the highest correlation with pSS disease activity. Therefore, this CXCL10 proteoform ratio represents an interesting exploratory disease activity biomarker to further investigate. As this strategy can be readily adapted to other plasma proteins and proteoforms of interest, we are convinced that it will lead to a more detailed understanding of proteoforms in physiology and pathology yielding more relevant biomarkers and drug targets.