Quantification Of Post-translational Modifications Research Articles

Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-Down Proteomics.

Ischemic cardiomyopathy (ICM) is a prominent form of heart failure, but the molecular mechanisms underlying ICM remain relatively understudied due to marked phenotypic heterogeneity. Alterations in post-translational modifications (PTMs) and isoform switches in sarcomeric proteins play important roles in cardiac pathophysiology. Thus, it is essential to define sarcomeric proteoform landscape to better understand ICM. Herein, we have implemented a top-down liquid chromatography (LC)-mass spectrometry (MS)-based proteomics method for the identification and quantification of sarcomeric proteoforms in the myocardia of donors without heart diseases (n = 16) compared to end-stage ICM patients (n = 16). Importantly, quantification of post-translational modifications (PTMs) and expression reveal significant changes in various sarcomeric proteins extracted from ICM tissues. Changes include altered phosphorylation and expression of cardiac troponin I (cTnI) and enigma homologue 2 (ENH2) as well as an increase in muscle LIM protein (MLP) and calsarcin-1 (Cal-1) phosphorylation in ICM hearts. Our results imply that the contractile apparatus of the sarcomere is severely dysregulated during ICM. Thus, this is the first study to uncover significant molecular changes to multiple sarcomeric proteins in the LV myocardia of the end-stage ICM patients using liquid chromatography-mass spectrometry (LC-MS)-based top-down proteomics. Raw data are available via the PRIDE repository with identifier PXD038066.

Characterization and quantification of post-translational modifications on proteins in cardiovascular disease

Characterization and quantification of post-translational modifications on proteins in cardiovascular disease

Fully automated peptide mapping multi-attribute method by liquid chromatography–mass spectrometry with robotic liquid handling system

The multi-attribute method (MAM) based on liquid chromatography (LC)–tandem mass spectrometry is emerging as a powerful tool to directly monitor multiple product quality attributes simultaneously. To better implement MAM, either for product characterization or for quality control (QC), there is a need for a robust, universal, and high-throughput workflow that can be broadly adopted in different laboratories with minimal barriers to implementation. Manual preparation of samples for MAM, however, is labor intensive and produces nontrivial variations across analysts and laboratories. We describe the development of a fully automated peptide mapping procedure with a high-throughput robotic liquid handling system to improve sample handling capacity and outcome reproducibility while saving analyst hands-on time. Our procedure features the automation of a “microdialysis” step, an efficient desalting approach prior to proteolytic digestion that optimizes digestion completeness and consistency each time. The workflow is completely hands-free and requires the analyst only to pre-normalize the sample concentrations and to load buffers and reagents at their designated positions on the robotic deck. The robotic liquid handler performs all the subsequent preparation steps and stores the digested samples on a chiller unit to await retrieval for further analysis. We also demonstrate that the manual and automated procedures are comparable with regard to protein sequence coverage, digestion completeness and consistency, and quantification of posttranslational modifications. Notably, in contrast to a previously reported automated sample preparation protocol that relied on customized accessories, all components in our automation procedure are commercial products that are readily available. In addition, we also present the high-throughput data analysis workflow by using Protein Metrics. The automation procedure can be applied cross-functionally in the biopharmaceutical industry and, given its practicality and reproducibility, can pave the way for MAM implementation in QC laboratories.

Integration of liquid chromatography mass spectrometry with a heavy peptide response curve accurately measures unprocessed C-terminal lysine during peptide mapping analysis of therapeutic antibodies in a single run

Therapeutic monoclonal and bispecific antibodies are susceptible to modification after protein biosynthesis. These post-translational modifications (PTMs) not only contribute to mass and charge heterogeneity, but they can also negatively impact the molecule’s activity, half-life, and immunogenicity. Therefore, identification and quantification of PTMs are critical to ensure the safety and efficacy of an antibody therapeutic as well as demonstrate product consistency and process control. Unprocessed C-terminal lysine on the heavy chain (HC) is a prevalent modification that contributes to this charge heterogeneity in antibodies. Peptide mapping through liquid chromatography tandem mass spectrometry (LC–MS2) enjoys higher selectivity and sensitivity for measuring this PTM relative to global PTM methods, but differences in the ionization efficiencies of the unprocessed C-terminal K peptide and the truncated C-terminal K peptide result in its overestimation. Consequently, large discrepancies in this PTM’s measured abundance may exist between different characterization assays used in regulatory filings, which can be further compounded by large variability when multiple mass spectrometers are used to quantify C-terminal K during a therapeutic’s lifespan. In this study, we propose a simple new method to quantify unprocessed C-terminal K in antibodies in a single LC–MS2 run that incorporates heavy isotopic standards for both the unprocessed and truncated C-terminal K peptide to build a response curve and correct for the disparity in ionization efficiency between these two different peptide sequences. The approach was evaluated across two different Orbitrap-based mass spectrometers using multiple monoclonal and bispecific therapeutic antibodies, resulting in accurate (<10% error, as determined with peptide standards) and precise C-terminal K quantification during peptide mapping analysis.

From proof of concept to the routine use of an automated and robust multi-dimensional liquid chromatography mass spectrometry workflow applied for the charge variant characterization of therapeutic antibodies

The identification and quantification of post-translational modifications (PTMs) is a crucial step required during the development of therapeutic proteins. In particular, the characterization of charge variants separated by cation exchange chromatography (CEX) is a tedious process commonly performed with an off-line manual fraction collection followed by peptide mapping. To improve the efficiency of this time-consuming approach, a generic on-line multi-dimensional LC/MS approach was developed for the characterization of various monoclonal antibody (mAb) isotypes and a bi-specific antibody (BsAb). Fractions collected from 1D CEX analysis were consecutively reduced on a 2D reversed phase liquid chromatography (RPLC) column (polyphenyl), digested within 1–2 min using a 3D immobilized trypsin cartridge, and finally the obtained peptides were separated on another 4D RPLC column (C18), and simultaneously identified with a Q Exactive™ mass spectrometer. 2D RPLC columns and 3D trypsin cartridges from different suppliers were compared, as well as the effects of reducing agents. The effect of 2D and 4D RPLC column temperature, and 2D RPLC column mass load were also systematically studied. Under optimal conditions, the multi-dimensional LC/MS system described in this paper is a robust tool for the on-line digestion of proteins and shows high repeatability. Similar levels of oxidation and deamidation were measured using the off-line and on-line approaches for the same stressed samples. The lower amounts of deamidation and isomerization measured at some asparagine and aspartic acid residues by the on-line approach compared to the manual off-line procedure suggest reduced artifacts using the on-line methodology. The multi-dimensional LC/MS described here enables fast, on-line, automated characterization of therapeutic antibodies without the need for off-line fraction collection and sample pre-treatment (manual approach). The entire workflow can be completed within less than one day, compared to weeks with the manual off-line procedure.

MON-213 Impact of post-translational modifications in chronic kidney disease and cardiovascular disease

Post-translational modifications of proteins and peptides have recently gained much attention, as they are involved in the pathogenesis of cardiovascular disease and eventually also in the progression of chronic kidney disease Here, we provide an overview of post-translational protein modifications such as carbamylation, glycation and oxidation, starting with their definitions, mechanisms and clinical relevance in the setting of chronic kidney disease and cardiovascular disease. The methods currently used for the identification and especially quantification of post-translational modifications are described and potential treatment options in the context of post-translational modifications are reviewed. We concluded that advancements in mass-spectrometry-based methods will certainly boost the clinical utility of sample analyses, leading to the identification of novel disease markers and/or pathophysiologically relevant factors.

SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.

SummaryMass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software package for the statistical analysis of high-throughput, quantitative proteomics experiments. SanXoT is based on our previously developed weighted spectrum, peptide and protein statistical model and has been specifically designed to be modular, scalable and user-configurable. SanXoT allows limitless workflows that adapt to most experimental setups, including quantitative protein analysis in multiple experiments, systems biology, quantification of post-translational modifications and comparison and merging of experimental data from technical or biological replicates.Availability and implementationDownload links for the SanXoT Software Package, source code and documentation are available at https://wikis.cnic.es/proteomica/index.php/SSP.Contact jvazquez@cnic.es or ebonzon@cnic.esSupplementary information Supplementary information is available at Bioinformatics online.

The future of LC-MS for pharmaceutical analysis: an interview with Jun Qu.

Jun Qu speaks to Sankeetha Nadarajah, Editor of Bioanalysis: Jun Qu is the group leader of the proteomics and pharmaceutical analysis lab of SUNY-Buffalo (NY, USA) and a Professor in the Department of Pharmaceutical Sciences. His research is focused on the study of Clinical and Pharmaceutical Proteomics and Pharmaceutical Analysis using LC-MS-based strategies. His research programs include high-resolution and large-scale expression profiling of pathological proteomes, for the discovery of novel disease/therapeutics biomarkers using gel-free proteomic methods; sensitive identification, localization and quantification of post-translational modifications in tissue proteomes such as these in myocardium, using novel anti-PTM affinity capture and alternating Collision-induced dissociation/Electron transfer dissociation to obtain abundant PTM information; targeted investigation of marker proteins that are of high interests for clinical and pharmaceutical study, using highly sensitive nano-LC/SRM-based methods; and highly sensitive and accurate investigation of the PK of biotherapeutics using LC-MS.

Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain.

Recent advances in mass spectrometry (MS)-based proteomics have greatly facilitated the robust identification and quantification of posttranslational modifications (PTMs), including those that are present at substoichiometric site occupancies. The abnormal posttranslational modification and accumulation of the microtubule-associated protein tau has been implicated in the pathogenesis of Alzheimer's disease (AD), and it is thought that the primary mode of regulation of tau occurs through PTMs. Several studies have been published regarding tau phosphorylation; however, other tau PTMs such as ubiquitylation, acetylation, methylation, oxidation, sumoylation, nitration, and glycosylation have not been analyzed as extensively. The comprehensive detection and delineation of these PTMs is critical for drug target discovery and validation. Lysine-directed PTMs including ubiquitylation, acetylation, and methylation play key regulatory roles with respect to the rates of tau turnover and aggregation. MS-based analytical approaches have been used to gain insight into the tau lysine-directed PTM signature that is most closely associated with neurofibrillary lesion formation. This chapter provides details pertaining to the liquid chromatography tandem mass spectrometry (LC-MS/MS)-based analysis of the lysine-directed posttranslational modification of tau.

Mass spectrometry profiling of non-enzymatic deamidation of articular cartilage components suggests slower protein turnover in deep regions and in hips compared with knees

Mass spectrometry profiling of non-enzymatic deamidation of articular cartilage components suggests slower protein turnover in deep regions and in hips compared with knees

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics.

Mass spectrometry has enabled the study of cellular signaling on a systems-wide scale, through the quantification of post-translational modifications, such as protein phosphorylation. Here we describe EasyPhos, a scalable phosphoproteomics platform that now allows rapid quantification of hundreds of phosphoproteomes in diverse cells and tissues at a depth of >10,000 sites. We apply this technology to generate time-resolved maps of insulin signaling in the mouse liver. Our results reveal that insulin affects ~10% of the liver phosphoproteome and that many known functional phosphorylation sites, and an even larger number of unknown sites, are modified at very early time points (<15 s after insulin delivery). Our kinetic data suggest that the flow of signaling information from the cell surface to the nucleus can occur on very rapid timescales of less than 1 min in vivo. EasyPhos facilitates high-throughput phosphoproteomics studies, which should improve our understanding of dynamic cell signaling networks and how they are regulated and dysregulated in disease.

Emerging role of post-translational modifications in chronic kidney disease and cardiovascular disease

Post-translational modifications (PTMs) of proteins and peptides have recently gained much attention, as they are involved in the pathogenesis of cardiovascular disease and eventually also play a role in the progression of chronic kidney disease (CKD). In this review, we provide an overview of post-translational protein modifications such as carbamylation, glycation and oxidation, starting with their definitions, mechanisms and clinical relevance in the setting of CKD and cardiovascular disease. The methods currently used for the identification and, in particular, quantification of PTMs are described and potential treatment options in the context of PTMs are reviewed. We foresee that advancements in mass spectrometry-based methods leading to the identification of novel disease markers and/or pathophysiologically relevant factors will certainly boost the clinical utility in sample analyses.

Proteomics of protein post-translational modifications implicated in neurodegeneration.

Mass spectrometry (MS)-based proteomics has developed into a battery of approaches that is exceedingly adept at identifying with high mass accuracy and precision any of the following: oxidative damage to proteins (redox proteomics), phosphorylation (phosphoproteomics), ubiquitination (diglycine remnant proteomics), protein fragmentation (degradomics), and other posttranslational modifications (PTMs). Many studies have linked these PTMs to pathogenic mechanisms of neurodegeneration. To date, identifying PTMs on specific pathology-associated proteins has proven to be a valuable step in the evaluation of functional alteration of proteins and also elucidates biochemical and structural explanations for possible pathophysiological mechanisms of neurodegenerative diseases. This review provides an overview of methods applicable to the identification and quantification of PTMs on proteins and enumerates historic, recent, and potential future research endeavours in the field of proteomics furthering the understanding of PTM roles in the pathogenesis of neurodegeneration.Electronic supplementary materialThe online version of this article (doi:10.1186/2047-9158-3-23) contains supplementary material, which is available to authorized users.

Consumption of Purple Sweet Potato Affects Post-Translational Modification of Plasma Proteins in Hamsters

A high level of intake of vegetables is strongly associated with the prevention of chronic diseases. Because post-translational modifications (PTMs) have been shown to be the important biomarkers of the change in physiological functions, this study aimed to explore the changes in PTMs of plasma proteins when purple sweet potato (PSP), a root vegetable, was incorporated into the daily diet. Male Syrian hamsters were maintained on a rice diet (50% rice) or PSP diet (25% rice and 25% PSP) for 12 weeks. Plasma proteins were fractionated by electrophoresis, digested by trypsin, and then separated by nano-liquid chromatography and tandem mass spectrometry. The TurboSequest algorithm was used to identify peptide sequence against the hamster database in Universal Proteins Resource Knowledgebase, and in-house PTM finder programs were used for identification and quantification of PTMs. The results indicated that 95 plasma proteins were identified and 28 PTM sites on 26 of these 95 proteins were affected by consumption of PSP (p < 0.05). Methylation accounted for the largest percentage of affected modifications (35.71%). This study also showed that incorporation of purple sweet potato into the diet significantly lowered blood and liver lipids (p < 0.05). The results of this study provide a basis for prospective studies evaluating the effects of dietary intervention on modifications of proteins.

Abstract 3997: Nanoproteomic analysis of extracellular receptor kinase-1/2 post-translational activation in microdissected human hyperplastic aberrant crypt foci.

Abstract Oncogenic activation resulting in hyperproliferative lesions within the colonic mucosa has been identified in putative precancerous lesions, aberrant crypt foci (ACF). KRAS (codons 12 and 13) and BRAFV600E mutation status was determined in 172 ACF identified in colorectum of screening subjects by in situ high-definition, magnifying chromoendoscopy. Lesions were stratified according to histology: serrated hyperplastic versus distended (non-serrated) hyperplastic. Due to their limiting size, however, it was not technically feasible to examine downstream signaling consequences of these oncogenic mutations. We have combined ultraviolet-infrared (UV/IR) micro-dissection with an ultra-sensitive nanofluidic proteomic immunoassay (NIA) to enable accurate quantification of post-translational modifications to mitogen-activated protein kinase (MAPK) in total protein lysates isolated from hyperproliferative crypts and adjacent normal mucosa. Using this approach, levels of singly and dually (activated) phosphorylated isoforms of extracellular receptor kinase(ERK)-1 and -2 were quantified in samples containing as little as 16-ng of total protein recovered from &amp;lt;200 colon epithelial cells. ERK activation is responsible for the observed hyperplasia found in these early lesions, but its activation state is not directly dependent on KRAS and/or BRAF mutation status. This study describes the novel use of a sensitive nanofluidic platform to measure oncogene-driven proteomic changes in diminutive lesions procured at the time of endoscopy and highlights the advantage of this approach over classical immunohistochemistry-based analyses. Citation Format: David A. Drew, Thomas Devers, Nicole Horelik, Shi Yang, Michael O'Brien, Rong Wu, Daniel W. Rosenberg. Nanoproteomic analysis of extracellular receptor kinase-1/2 post-translational activation in microdissected human hyperplastic aberrant crypt foci. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3997. doi:10.1158/1538-7445.AM2013-3997

Automated in-solution protein digestion using a commonly available high-performance liquid chromatography autosampler

A completely automated peptide mapping liquid chromatography/mass spectrometry (LC/MS) system for characterization of therapeutic proteins in which a common high-performance liquid chromatography (HPLC) autosampler is used for automated sample preparation, including protein denaturation, reduction, alkylation, and enzymatic digestion, is described. The digested protein samples are then automatically subjected to LC/MS analysis using the same HPLC system. The system was used for peptide mapping of monoclonal antibodies (mAbs), known as a challenging group of therapeutic proteins for achieving complete coverage and quantitative representation of all peptides. Detailed sample preparation protocols, using an Agilent HPLC system, are described for Lys-C digestion of mAbs with intact disulfide bonds and tryptic digestion of mAbs after reduction and alkylation. The automated procedure of Lys-C digestion of nonreduced antibody, followed by postdigestion disulfide reduction, produces both the nonreduced and reduced digests that facilitate disulfide linkage analysis. The automated peptide mapping LC/MS system has great utility in preparing and analyzing multiple samples for protein characterization, identification, and quantification of posttranslational modifications during process and formulation development as well as for protein identity and quality control.

In-gel stable isotope labeling for relative quantification using mass spectrometry

Although differences in protein staining intensity can often be visualized by difference gel electrophoresis, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. We present a protocol for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using in-gel stable isotope labeling. In this protocol protein extracts from any source treated under two experimental conditions are resolved in two separate lanes by gel electrophoresis. Parallel gel regions of interest are reacted separately with either light or heavy isotope-labeled reagents, and the gel slices are then combined and digested with proteases. The resulting peptides are then analyzed by liquid chromatography/mass spectrometry (LC/MS) to determine relative abundance of light- and heavy-isotope lysine-containing peptide pairs and analyzed by LC/MS/MS for identification of sequence and modifications. This protocol should take approximately 24-26 h to complete, including the incubation time for proteolytic digestion. Additional time will be needed for data analysis and interpretation.

In-Gel Stable-Isotope Labeling (ISIL): A Strategy for Mass Spectrometry-Based Relative Quantification

Most proteomics approaches for relative quantification of protein expression use a combination of stable-isotope labeling and mass spectrometry. Traditionally, researchers have used difference gel electrophoresis (DIGE) from stained 1D and 2D gels for relative quantification. While differences in protein staining intensity can often be visualized, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. A method is presented for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using In-gel Stable-Isotope Labeling (ISIL). Proteins extracted from any source (tissue, cell line, immunoprecipitate, etc.), treated under two experimental conditions, are resolved in separate lanes by gel electrophoresis. The regions of interest (visualized by staining) are reacted separately with light versus heavy isotope-labeled reagents, and the gel slices are then mixed and digested with proteases. The resulting peptides are then analyzed by LC-MS to determine relative abundance of light/heavy isotope pairs and analyzed by LC-MS/MS for identification of sequence and modifications. The strategy compares well with other relative quantification strategies, and in silico calculations reveal its effectiveness as a global relative quantification strategy. An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification.

Drug Research

A completely automated peptide mapping liquid chromatography/mass spectrometry (LC/MS) system for characterization of therapeutic proteins in which a common high-performance liquid chromatography (HPLC) autosampler is used for automated sample preparation, including protein denaturation, reduction, alkylation, and enzymatic digestion, is described. The digested protein samples are then automatically subjected to LC/MS analysis using the same HPLC system. The system was used for peptide mapping of monoclonal antibodies (mAbs), known as a challenging group of therapeutic proteins for achieving complete coverage and quantitative representation of all peptides. Detailed sample preparation protocols, using an Agilent HPLC system, are described for Lys-C digestion of mAbs with intact disulfide bonds and tryptic digestion of mAbs after reduction and alkylation. The automated procedure of Lys-C digestion of nonreduced antibody, followed by postdigestion disulfide reduction, produces both the nonreduced and reduced digests that facilitate disulfide linkage analysis. The automated peptide mapping LC/MS system has great utility in preparing and analyzing multiple samples for protein characterization, identification, and quantification of posttranslational modifications during process and formulation development as well as for protein identity and quality control.

Proteomic analysis of the basic proteins in 5-fluorouracil resistance of human colon cancer cell line using the radical-free and highly reducing method of two-dimensional polyacrylamide gel electrophoresis

5-Fluorouracil (5-FU) is widely used for the treatment of patients with advanced colon cancers and it is the mainstay of chemotherapy. However, the acquisition of resistance to 5-FU is one of the most prominent obstacles to successful chemotherapy. The purpose of this study was to identify the novel biological basis of 5-FU resistance in colon cancer cells. This study is the first comparative proteomic analysis of basic proteins between the DLD-1 human colon cancer cell line and DLD-1/5-FU its 5-FU resistant sub-line using the radical-free and highly reducing method of two-dimensional polyacrylamide gel electrophoresis, which has a superior ability in the separation of basic proteins and the quantification of post-translational modification. A densitometric analysis was performed to quantify the modulated proteins, and protein spots showing significant changes were identified by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Six basic proteins significantly modulated between DLD-1 and DLD-1/5-FU were identified. All of them showed up-regulated expression in DLD-1/5-FU in comparison to DLD-1. The six identified spots, corresponding to five different proteins included heterogeneous nuclear ribonucleoprotein G, mitochondrial transcription factor A, histone H2B, histone H4 and ribosomal protein L3. Among the 5 basic proteins, several proteins are potentially related to 5-FU resistance by protecting the cells from DNA damage.