Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics

Pirmoradian, Mohammad; Budamgunta, Harshavardhan; Chingin, Konstantin; Zhang, Bo; Astorga‐Wells, Juan; Zubarev, Roman A.

doi:10.1074/mcp.o113.028787

Cited by 132 publications

(163 citation statements)

References 33 publications

Supporting

Mentioning

148

Contrasting

Unclassified

Order By: Relevance

“…As a result, distinct regions on the proteome microarray can be made highly homogeneous in terms of surface protein densities, with a dynamic range of protein amount per spot of less than 10 2 (11). In contrast, at a given time point, at least 5,000 proteins are detectable by MS with a dynamic range of 10 7 (22). Thus, by using the human proteome microarray, three times more proteins can be screened at high confidence in a single experiment.…”

Section: Discussionmentioning

confidence: 99%

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic

Zhang

Yang

Ling

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

134

101

View full text Add to dashboard Cite

Arsenic is highly effective for treating acute promyelocytic leukemia (APL) and has shown significant promise against many other tumors. However, although its mechanistic effects in APL are established, its broader anticancer mode of action is not understood. In this study, using a human proteome microarray, we identified 360 proteins that specifically bind arsenic. Among the most highly enriched proteins in this set are those in the glycolysis pathway, including the rate-limiting enzyme in glycolysis, hexokinase-1. Detailed biochemical and metabolomics analyses of the highly homologous hexokinase-2 (HK2), which is overexpressed in many cancers, revealed significant inhibition by arsenic. Furthermore, overexpression of HK2 rescued cells from arsenic-induced apoptosis. Our results thus strongly implicate glycolysis, and HK2 in particular, as a key target of arsenic. Moreover, the arsenic-binding proteins identified in this work are expected to serve as a valuable resource for the development of synergistic antitumor therapeutic strategies.arsenic trioxide | human proteome microarray | glycolysis | hexokinase-2IA rsenic and its derivatives have been applied as therapy for a variety of diseases for more than 2,200 y (1). To date, the disease most successfully treated with these types of compounds is acute promyelocytic leukemia (APL). Administration of arsenic trioxide (ATO) combined with all-trans retinoic acid has demonstrated a remarkable 5-y overall survival rate of 85-90% as a consequence of the dramatic down-regulation of the key protein driving APL tumorigenicity, promyelocytic leukemia-retinoic acid receptor α (PML-RARα) (2). However, ATO also has been found to be effective against many other hematologic malignancies and solid tumors. For example, together with imatinib it is a promising treatment for chronic myelocytic leukemia (3), and it has been used alone with some success to treat multiple myeloma (4), myelodysplasia syndrome (5), and non-Hodgkin lymphoma (6). ATO also is under clinical investigation as a possible medication for lung cancer, hepatocellular carcinoma, melanoma, renal cell carcinoma, and colorectal cancer (https://www.clinicaltrials.gov/). At the cellular level, ATO has been shown to inhibit significantly the growth of almost all the cell lines (59 of 60) in the US National Cancer Institute anticancer drug screen that spans nine different tumor types (7). Thus ATO is one of the most promising broadly effective medications against cancer.Although its mode of action in APL is well established, the underlying mechanisms by which ATO acts in other types of cancers remain poorly understood. A variety of systematic studies, including studies that provided transcriptomic, chemogenomic, or proteomic characterizations (8, 9), have been performed to gain a better understanding of this broader anticancer activity of ATO. However, these studies examined only the cellular consequences of treatment with ATO without identifying the primary proteins directly bound and modulated by ATO. Knowledge of ATO...

show abstract

Section: Discussionmentioning

confidence: 99%

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic

Zhang

Yang

Ling

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

134

101

View full text Add to dashboard Cite

show abstract

“…In this work, we describe the most complete secretome (228 proteins including Rips) of a plant pathogenic bacterium using a MS-based shotgun approach with a label-free quantification (24). This allowed us to compare secretomes between hpa (hrp-associated) mutants and evaluate their respective involvement in T3S.…”

mentioning

confidence: 99%

Comparative Secretome Analysis of Ralstonia solanacearum Type 3 Secretion-Associated Mutants Reveals a Fine Control of Effector Delivery, Essential for Bacterial Pathogenicity

Lonjon

Turner

Henry

et al. 2016

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

Ralstonia solanacearum, the causal agent of bacterial wilt, exerts its pathogenicity through more than a hundred secreted proteins, many of them depending directly on the functionality of a type 3 secretion system. To date, only few type 3 effectors have been identified as required for bacterial pathogenicity, notably because of redundancy among the large R. solanacearum effector repertoire. In order to identify groups of effectors collectively promoting disease on susceptible hosts, we investigated the role of putative post-translational regulators in the control of type 3 secretion. A shotgun secretome analysis with label-free quantification using tandem mass spectrometry was performed on the R. solanacearum GMI1000 strain. There were 228 proteins identified, among which a large proportion of type 3 effectors, called Rip (Ralstonia injected proteins). Thanks to this proteomic approach, RipBJ was identified as a new effector specifically secreted through type 3 secretion system and translocated into plant cells. A focused Rip secretome analysis using hpa (hypersensitive response and pathogenicity associated) mutants revealed a fine secretion regulation and specific subsets of Rips with different secretion patterns. We showed that a set of Rips (RipF1, RipW, RipX, RipAB, and RipAM) are secreted in an Hpa-independent manner. We hypothesize that these Rips could be preferentially involved in the first stages of type 3 secretion. In addition, the secretion of about thirty other Rips is controlled by HpaB and HpaG. HpaB, a candidate chaperone was shown to positively control secretion of numerous Rips, whereas HpaG was shown to act as a negative regulator of secretion. To evaluate the impact of altered type 3 effectors secretion on plant pathogenesis, the hpa mutants were assayed on several host plants. HpaB was required for bacterial pathogenicity on multiple hosts whereas HpaG was found to be specifically required for full R. solanacearum pathogenicity on the legume plant Medicago truncatula. Molecular & Cellular Proteomics 15: 10.1074/ mcp.M115.051078, 598-613, 2016.The soil-borne vascular bacterium R. solanacearum is described as one of the most destructive plant pathogenic bacterium worldwide (1), mainly because of its broad host range and wide geographic distribution. Indeed, R. solanacearum attacks more than 250 plant species, distributed in more than 50 botanical families (2). R. solanacearum causes dramatic crop losses, more specifically in the tropics, notably affecting emerging countries. Durable protection strategies against this bacterium are lacking. R. solanacearum penetrates into the plant via the roots, and then colonizes the xylem vessels. The bacterium reaches the aerial parts of the plant, causes wilting symptoms leading to the death of the plant, and will eventually return to the soil, completing the cycle (3). To achieve these first colonization steps, the bacterium uses a molecular syringe called the type 3 secretion system (T3SS), 1 which deFrom the ‡INRA, Laboratoire des Interactions Plantes-...

show abstract

“…Discovery proteomics, relying on nonsupervised data dependent acquisition (DDA), is routinely used to effectively profile, with broad coverage, the proteome under investigation (1,2). This strategy is focused on protein identification but has limitations with respect to quantitative applications.…”

mentioning

confidence: 99%

Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)*

Gallien

Kim

Domon

2015

Molecular & Cellular Proteomics

178

185

View full text Add to dashboard Cite

Targeted high-resolution and accurate mass analyses performed on fast sequencing mass spectrometers have opened new avenues for quantitative proteomics. More specifically, parallel reaction monitoring (PRM) implemented on quadrupole-orbitrap instruments exhibits exquisite selectivity to discriminate interferences from analytes. Furthermore, the instrument trapping capability enhances the sensitivity of the measurements. The PRM technique, applied to the analysis of limited peptide sets (typically 50 peptides or less) in a complex matrix, resulted in an improved detection and quantification performance as compared with the reference method of selected reaction monitoring performed on triple quadrupole instruments. However, the implementation of PRM for the analysis of large peptide numbers requires the adjustment of mass spectrometry acquisition parameters, which affects dramatically the quality of the generated data, and thus the overall output of an experiment. A newly designed data acquisition scheme enabled the analysis of moderate-to-large peptide numbers while retaining a Liquid chromatography (LC) 1 coupled to tandem mass spectrometry (MS/MS) approaches have been widely acknowledged as one of the most effective methods to study complex proteomes. In particular, their preclinical, and also clinical applications, have contributed to advances in biomedical sciences. A bottom-up proteomics workflow relies on the enzymatic digestion of the proteins constituting a proteome to generate thousands of peptides, which are subsequently separated by liquid chromatography and analyzed by tandem mass spectrometry. Two main MS-based strategies have emerged from this generic process, which differ in their objectives and acquisition schemes and are commonly referred to as discovery and targeted strategies, respectively; both presenting advantages and drawbacks to study specific biological and clinical questions.Discovery proteomics, relying on nonsupervised data dependent acquisition (DDA), is routinely used to effectively profile, with broad coverage, the proteome under investigation (1, 2). This strategy is focused on protein identification but has limitations with respect to quantitative applications. The stochastic nature of DDA sampling results in "missing values" in replicated experiments, directly affecting quantitative studies, whereas low abundance components remain largely undetected (3). By contrast, targeted proteomics has emerged to more systematically quantify peptides/proteins present in a wide range of concentrations in complex samples (4). The hypothesis-driven nature of targeted data acquisition (TDA), where the peptides used as surrogates for a preselected set of proteins are consistently measured across a multitude of

show abstract

Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics

Cited by 132 publications

References 33 publications

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic

Comparative Secretome Analysis of Ralstonia solanacearum Type 3 Secretion-Associated Mutants Reveals a Fine Control of Effector Delivery, Essential for Bacterial Pathogenicity

Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)*

Contact Info

Product

Resources

About