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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 52978

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Prof. Dr. Paolo Iadarola

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Department of Biology and Biotechnology “L. Spallanzani”, Universita degli Studi di Pavia, Pavia, Italy
Interests: purification and characterization of enzymes and structural proteins; investigation of the proteome of different tissues/fluids by using the conventional methods of proteomics/metabolomics
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Dear Colleagues,

A comprehensive understanding of the biochemical processes that govern life requires a deep understanding of the information encoded in the genome, and that relate to all protein forms expressed in a biological system, i.e., the proteome. While being complementary to each other, only proteome, that differs from cell to cell and changes, even for a single cell, in response to different stimuli, is descriptive of a biological phenotype. Detecting and quantifying all proteins, studying their post-translational modifications, level of expression, localization, interaction, and domain structure are the goals of proteomics. Because of its ability to handle the complexity of the events mentioned above, mass spectrometry (MS) has become an indispensable tool for proteomics. However, what does the term MS stand for? MS consists of a variety of analytical methods, each characterized by its own strengths for the solution of a peculiar problem and of which the choice depends on the aim of the study. The numerous developed applications of MS in proteomics, thus far, have contributed heavily to new insights into the roles played by some proteins in human disorders.

The aim of this Special Issue is to attract contributions on all aspects of MS-based proteomics with a special emphasis on recent/novel technologies that, by pushing the boundary of MS capabilities, make them able to address biological problems that have not yet been faced.

Prof. Dr. Paolo Iadarola
Guest Editor

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Keywords

proteome
mass spectrometry
biological system
genome
protein forms
biological phenotype
expression, localization, interaction and domain structure of proteomics

Published Papers (11 papers)

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Editorial

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3 pages, 148 KiB

Open AccessEditorial

Special Issue: Mass Spectrometric Proteomics

by Paolo Iadarola

Molecules 2019, 24(6), 1133; https://doi.org/10.3390/molecules24061133 - 21 Mar 2019

Cited by 6 | Viewed by 1797

Abstract

The term “Proteomics” refers to the characterization of the proteome, that is, all proteins present in a biological system [...] Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

Research

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18 pages, 3611 KiB

Open AccessFeature PaperArticle

Urinary Proteomics Profiles Are Useful for Detection of Cancer Biomarkers and Changes Induced by Therapeutic Procedures

by Emanuele Ferrari, Andrea Wittig, Fabrizio Basilico, Rossana Rossi, Antonella De Palma, Dario Di Silvestre, Wolfgang A.G. Sauerwein and Pier Luigi Mauri

Molecules 2019, 24(4), 794; https://doi.org/10.3390/molecules24040794 - 22 Feb 2019

Cited by 25 | Viewed by 4742

Abstract

Boron neutron capture therapy (BNCT) is a binary cancer treatment modality where two different agents (¹⁰B and thermal neutrons) have to be present to produce an effect. A dedicated trial design is necessary for early clinical trials. The concentration of ¹⁰B in tissues is an accepted surrogate to predict BNCT effects on tissues. Tissue, blood, and urines were sampled after infusion of two different boron carriers, namely BSH and BPA in the frame of the European Organisation for Research and Treatment of Cancer (EORTC) trial 11001. In this study, urine samples were used to identify protein profiles prior and after drug infusion during surgery. Here, an approach that is based on the mass spectrometry (MS)-based proteomic analysis of urine samples from head and neck squamous cell carcinoma (HNSCC) and thyroid cancer patients is presented. This method allowed the identification of several inflammation- and cancer-related proteins, which could serve as tumor biomarkers. In addition, changes in the urinary proteome during and after therapeutic interventions were detected. In particular, a reduction of three proteins that were involved in inflammation has been observed: Galectin-3 Binding Protein, CD44, and osteopontin. The present work represents a proof of principle to follow proteasome changes during complex treatments based on urine samples. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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20 pages, 3018 KiB

Open AccessFeature PaperArticle

Proteome Investigation of Rat Lungs Subjected to Ex Vivo Perfusion (EVLP)

by Valentina Roffia, Antonella De Palma, Caterina Lonati, Dario Di Silvestre, Rossana Rossi, Marco Mantero, Stefano Gatti, Daniele Dondossola, Franco Valenza, Pierluigi Mauri and Francesco Blasi

Molecules 2018, 23(12), 3061; https://doi.org/10.3390/molecules23123061 - 22 Nov 2018

Cited by 17 | Viewed by 3344

Abstract

Ex vivo lung perfusion (EVLP) is an emerging procedure that allows organ preservation, assessment and reconditioning, increasing the number of marginal donor lungs for transplantation. However, physiological and airflow measurements are unable to unveil the molecular mechanisms responsible of EVLP beneficial effects on lung graft and monitor the proper course of the treatment. Thus, it is urgent to find specific biomarkers that possess these requirements but also accurate and reliable techniques that identify them. The purpose of this study is to give an overview on the potentiality of shotgun proteomic platforms in characterizing the status and the evolution of metabolic pathways during EVLP in order to find new potential EVLP-related biomarkers. A nanoLC-MS/MS system was applied to the proteome analysis of lung tissues from an optimized rat model in three experimental groups: native, pre- and post-EVLP. Technical and biological repeatability were evaluated and, together with clustering analysis, underlined the good quality of data produced. In-house software and bioinformatics tools allowed the label-free extraction of differentially expressed proteins among the three examined conditions and the network visualization of the pathways mainly involved. These promising findings encourage further proteomic investigations of the molecular mechanisms behind EVLP procedure. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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17 pages, 5333 KiB

Open AccessArticle

Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)

by Zhiyong Li, Yifeng Wang, Babatunde Kazeem Bello, Abolore Adijat Ajadi, Xiaohong Tong, Yuxiao Chang and Jian Zhang

Molecules 2018, 23(11), 2843; https://doi.org/10.3390/molecules23112843 - 01 Nov 2018

Cited by 6 | Viewed by 2980

Abstract

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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22 pages, 2800 KiB

Open AccessArticle

Optimisation of Milk Protein Top-Down Sequencing Using In-Source Collision-Induced Dissociation in the Maxis Quadrupole Time-of-Flight Mass Spectrometer

by Delphine Vincent, Dominik Mertens and Simone Rochfort

Molecules 2018, 23(11), 2777; https://doi.org/10.3390/molecules23112777 - 26 Oct 2018

Cited by 11 | Viewed by 3621

Abstract

Top-down sequencing in proteomics has come of age owing to continuous progress in LC-MS. With their high resolution and broad mass range, Quadrupole Time-of-Flight (Q-ToF) hybrid mass spectrometers equipped with electrospray ionisation source and tandem MS capability by collision-induced dissociation (CID) can be employed to analyse intact proteins and retrieve primary sequence information. To our knowledge, top-down proteomics methods with Q-ToF have only been evaluated using samples of relatively low complexity. Furthermore, the in-source CID (IS-CID) capability of Q-ToF instruments has been under-utilised. This study aimed at optimising top-down sequencing of intact milk proteins to achieve the greatest sequence coverage possible from samples of increasing complexity, assessed using nine known proteins. Eleven MS/MS methods varying in their IS-CID and conventional CID parameters were tested on individual and mixed protein standards as well as raw milk samples. Top-down sequencing results from the nine most abundant proteoforms of caseins, alpha-lactalbumin and beta-lactoglubulins were compared. Nine MS/MS methods achieved more than 70% sequence coverage overall to distinguish between allelic proteoforms, varying only by one or two amino acids. The optimal methods utilised IS-CID at low energy. This experiment demonstrates the utility of Q-ToF systems for top-down proteomics and that IS-CID could be more frequently employed. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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14 pages, 1121 KiB

Open AccessArticle

Comparative Proteomic Analysis of Rana chensinensis Oviduct

by Hang Su, He Zhang, Xinghua Wei, Daian Pan, Li Jing, Daqing Zhao, Yu Zhao and Bin Qi

Molecules 2018, 23(6), 1384; https://doi.org/10.3390/molecules23061384 - 08 Jun 2018

Cited by 8 | Viewed by 5527

Abstract

As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique. Then, all identified proteins were used to obtain gene ontology (GO) annotation. Ultimately, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis was performed to predict the pathway on differentially expressed proteins (DEPs). A total of 4479 proteins were identified, and 312 of them presented different expression profiling between prehibernation and breeding period. Compared with prehibernation group, 86 proteins were upregulated, and 226 proteins were downregulated in breeding period. After KEGG enrichment analysis, 163 DEPs were involved in 6 pathways, which were lysosome, RNA transport, glycosaminoglycan degradation, extracellular matrix (ECM)–receptor interaction, metabolic pathways and focal adhesion. This is the first report on the protein profiling of Rana chensinensis oviduct during the breeding period and prehibernation. Results show that this distinctive physiological phenomenon of Rana chensinensis oviduct was mainly involved in ECM–receptor interaction, metabolic pathways, and focal adhesion. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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14 pages, 2793 KiB

Open AccessArticle

Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803

by Yuma Tokumaru, Kiyoka Uebayashi, Masakazu Toyoshima, Takashi Osanai, Fumio Matsuda and Hiroshi Shimizu

Molecules 2018, 23(5), 1051; https://doi.org/10.3390/molecules23051051 - 01 May 2018

Cited by 16 | Viewed by 5460

Abstract

A targeted proteome analysis was conducted to investigate the SigE dependent-regulation of central metabolism in Synechocystis sp. PCC 6803 by directly comparing the protein abundance profiles among the wild type, a sigE deletion mutant (ΔsigE), and a sigE over-expression (sigEox) strains. Expression levels of 112 target proteins, including the central metabolism related-enzymes and the subunits of the photosystems, were determined by quantifying the tryptic peptides in the multiple reaction monitoring (MRM) mode of liquid-chromatography–triple quadrupole mass spectrometry (LC–MS/MS). Comparison with gene-expression data showed that although the abundance of Gnd protein was closely correlated with that of gnd mRNA, there were poor correlations for GdhA/gdhA and glycogen degradation-related genes such as GlgX/glgX and GlgP/glgP pairs. These results suggested that the regulation of protein translation and degradation played a role in regulating protein abundance. The protein abundance profile suggested that SigE overexpression reduced the proteins involved in photosynthesis and increased GdhA abundance, which is involved in the nitrogen assimilation pathway using NADPH. The results obtained in this study successfully demonstrated that targeted proteome analysis enables direct comparison of the abundance of central metabolism- and photosystem-related proteins. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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21 pages, 5143 KiB

Open AccessArticle

Identification of Ophiocordyceps sinensis and Its Artificially Cultured Ophiocordyceps Mycelia by Ultra-Performance Liquid Chromatography/Orbitrap Fusion Mass Spectrometry and Chemometrics

by Ping Zhang, Saina Li, Juan Li, Feng Wei, Xianlong Cheng, Guifeng Zhang, Shuangcheng Ma and Bin Liu

Molecules 2018, 23(5), 1013; https://doi.org/10.3390/molecules23051013 - 26 Apr 2018

Cited by 10 | Viewed by 5176

Abstract

Since the cost of Ophiocordyceps sinensis, an important fungal drug used in Chinese medicine, has increased dramatically, and the counterfeits may have adverse health effects, a rapid and precise marker using the peptide mass spectrometry identification system could significantly enhance the regulatory capacity. In this study, we determined the marker peptides in the digested mixtures of fungal proteins in wild O. sinensis fruiting bodies and various commercially available mycelium fermented powders using ultra-performance liquid chromatography/Orbitrap Fusion mass spectrometry coupled with chemometrics. The results indicated the following marker peptides: TLLEAIDSIEPPK (m/z 713.39) was identified in the wild O. sinensis fruiting body, AVLSDAITLVR (m/z 579.34) was detected in the fermented O. sinensis mycelium powder, FAELLEK (m/z 849.47) was found in the fermented Ophiocordyceps mycelium powder, LESVVTSFTK (m/z 555.80) was discovered in the artificial Ophiocordyceps mycelium powder, and VPSSAVLR (m/z 414.75) was observed in O. mortierella mycelium powder. In order to verify the specificity and applicability of the method, the five marker peptides were synthesized and tested on all samples. All in all, to the best of our knowledge, this is the first time that mass spectrometry has been employed to detect the marker peptides of O.sinensis and its related products. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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Review

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19 pages, 2996 KiB

Open AccessReview

Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics

by Remigiusz Bąchor, Mateusz Waliczek, Piotr Stefanowicz and Zbigniew Szewczuk

Molecules 2019, 24(4), 701; https://doi.org/10.3390/molecules24040701 - 15 Feb 2019

Cited by 49 | Viewed by 5878

Abstract

Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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17 pages, 3302 KiB

Open AccessReview

Elucidation of the Mechanism of Action for Metal Based Anticancer Drugs by Mass Spectrometry-Based Quantitative Proteomics

by Shuailong Jia, Runjing Wang, Kui Wu, Hongliang Jiang and Zhifeng Du

Molecules 2019, 24(3), 581; https://doi.org/10.3390/molecules24030581 - 06 Feb 2019

Cited by 19 | Viewed by 4610

Abstract

The discovery of the anticancer activity of cisplatin and its clinical application has opened a new field for studying metal-coordinated anticancer drugs. Metal-based anticancer drugs, such as cisplatin, can be transported to cells after entering into the human body and form metal–DNA or metal–protein adducts. Then, responding proteins will recognize adducts and form stable complexes. The proteins that were binding with metal-based anticancer drugs were relevant to their mechanism of action. Herein, investigation of the recognition between metal-based anticancer drugs and its binding partners will further our understanding about the pharmacology of cytotoxic anticancer drugs and help optimize the structure of anticancer drugs. The “soft” ionization mass spectrometric methods have many advantages such as high sensitivity and low sample consumption, which are suitable for the analyses of complex biological samples. Thus, MS has become a powerful tool for the identification of proteins binding or responding to metal-based anticancer drugs. In this review, we focused on the mass spectrometry-based quantitative strategy for the identification of proteins specifically responding or binding to metal-based anticancer drugs, ultimately elucidating their mechanism of action. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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14 pages, 2466 KiB

Open AccessReview

Pseudotrypsin: A Little-Known Trypsin Proteoform

by Zdeněk Perutka and Marek Šebela

Molecules 2018, 23(10), 2637; https://doi.org/10.3390/molecules23102637 - 14 Oct 2018

Cited by 25 | Viewed by 9034

Abstract

Trypsin is the protease of choice for protein sample digestion in proteomics. The most typical active forms are the single-chain β-trypsin and the two-chain α-trypsin, which is produced by a limited autolysis of β-trypsin. An additional intra-chain split leads to pseudotrypsin (ψ-trypsin) with three chains interconnected by disulfide bonds, which can be isolated from the autolyzate by ion-exchange chromatography. Based on experimental data with artificial substrates, peptides, and protein standards, ψ-trypsin shows altered kinetic properties, thermodynamic stability and cleavage site preference (and partly also cleavage specificity) compared to the above-mentioned proteoforms. In our laboratory, we have analyzed the performance of bovine ψ-trypsin in the digestion of protein samples with a different complexity. It cleaves predominantly at the characteristic trypsin cleavage sites. However, in a comparison with common tryptic digestion, non-specific cleavages occur more frequently (mostly after the aromatic residues of Tyr and Phe) and more missed cleavages are generated. Because of the preferential cleavages after the basic residues and more developed side specificity, which is not expected to occur for the major trypsin forms (but may appear anyway because of their autolysis), ψ-trypsin produces valuable information, which is complementary in part to data based on a strictly specific trypsin digestion and thus can be unnoticed following common proteomics protocols. Full article

(This article belongs to the Special Issue Mass Spectrometric Proteomics)

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