Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics

Electron transfer dissociation (ETD) has been developed recently as an efficient ion fragmentation technique in mass spectrometry (MS), being presently considered a step forward in proteomics with real perspectives for improvement, upgrade and application. Available also on affordable ion trap mass spectrometers, ETD induces specific N–Cα bond cleavages of the peptide backbone with the preservation of the post-translational modifications and generation of product ions that are diagnostic for the modification site(s). In addition, in the last few years ETD contributed significantly to the development of top-down approaches which enable tandem MS of intact protein ions. The present review, covering the last 5 years highlights concisely the major achievements and the current applications of ETD fragmentation technique in proteomics. An ample part of the review is dedicated to ETD contribution in the elucidation of the most common posttranslational modifications, such as phosphorylation and glycosylation. Further, a brief section is devoted to top-down by ETD method applied to intact proteins. As the last few years have witnessed a major expansion of the microfluidics systems, a few considerations on ETD in combination with chip-based nanoelectrospray (nanoESI) as a platform for high throughput top-down proteomics are also presented.     

Characterization of a high field Orbitrap mass spectrometer for proteome analysis

The field of proteomics continues to be driven by improvements in analytical technology, notably in peptide separation, quantitative MS, and informatics. In this study, we have characterized a hybrid linear ion trap high field Orbitrap mass spectrometer (Orbitrap Elite) for proteomic applications. The very high resolution available on this instrument allows 95% of all peptide masses to be measured with sub‐ppm accuracy that in turn improves protein identification by database searching. We further confirm again that mass accuracy in tandem mass spectra is a valuable parameter for improving the success of protein identification. The new CID rapid scan type of the Orbitrap Elite achieves similar performance as higher energy collision induced dissociation fragmentation and both allow the identification of hundreds of proteins from as little as 0.1 ng of protein digest on column. The new instrument outperforms its predecessor the Orbitrap Velos by a considerable margin on each metric assessed that makes it a valuable and versatile tool for MS‐based proteomics.     

Mass spectrometry for high throughput quantitative proteomics in plant research: lessons from thylakoid membranes

Proteomics seeks to monitor the flux of protein through cells under variable developmental and environmental influences as programmed by the genome. Consequently, it is necessary to measure changes in protein abundance and turnover rate as faithfully as possible. In the absence of non-invasive technologies, the majority of proteomics approaches involve destructive sampling at various time points to obtain 'snapshots' that periodically report the genomes's product. The work has fallen to separations technologies coupled to mass spectrometry, for high throughput protein identification. Quantitation has become the major challenge facing proteomics as the field matures. Because of the variability of day-to-day measurements of protein quantities by mass spectrometry, a common feature of quantitative proteomics is the use of stable isotope coding to distinguish control and experimental samples in a mixture that can be profiled in a single experiment. To address limitations with separation technologies such as 2D-gel electrophoresis, alternative systems are being introduced including multi-dimensional chromatography. Strategies that accelerate throughput for mass spectrometry are also emerging and the benefits of these 'shotgun' protocols will be considered in the context of the thylakoid membrane and photosynthesis. High resolution Fourier-transform mass spectrometry is bringing increasingly accurate mass measurements to peptides and a variety of gas-phase dissociation mechanisms are permitting 'top-down' sequencing of intact proteins. Finally, a versatile workflow for sub-cellular compartments including membranes is presented that allows for intact protein mass measurements, localization of post-translational modifications and relative quantitation or turnover measurement.     

Membrane‐Based SDS Depletion Ahead of Peptide and Protein Analysis by Mass Spectrometry

SDS interferes with both bottom‐up and top‐down MS analysis, requiring removal prior to detection. Filter‐aided sample preparation (FASP) is favored for bottom‐up proteomics (BUP) while acetone precipitation is popular for top‐down proteomics (TDP). We recently demonstrated acetone precipitation in a membrane filter cartridge. Alternatively, our automated electrophoretic device, termed transmembrane electrophoresis (TME), depletes SDS for both TDP and BUP studies. Here TME is compared to these two alternative methods of SDS depletion in both BUP and TDP workflows. To do so, a modified FASP method is described applicable to the SDS purification and recovery of intact proteins, suitable for LC/MS. All three methods reliably deplete >99.8% SDS. TME provide higher sample yields (average 90%) than FASP (55%) or acetone precipitation (57%), translating into higher total protein identifications (973 vs 877 FASP or 890 acetone) and higher spectral matches (2.5 times) per protein. In a top down workflow, each SDS‐depletion method yields high‐quality MS spectra for intact proteins. These results show each of these membrane‐based strategies is capable of depleting SDS with high sample recovery and high spectra quality for both BUP and TDP studies.     

Functional genomics by mass spectrometry

Systematic analysis of the function of genes can take place at the oligonucleotide or protein level. The latter has the advantage of being closest to function, since it is proteins that perform most of the reactions necessary for the cell. For most protein based ('proteomic') approaches to gene function, mass spectrometry is the method of choice. Mass spectrometry can now identify proteins with very high sensitivity and medium to high throughput. New instrumentation for the analysis of the proteome has been developed including a MALDI hybrid quadrupole time of flight instrument which combines advantages of the mass finger printing and peptide sequencing methods for protein identification. New approaches include the isotopic labeling of proteins to obtain accurate quantitative data by mass spectrometry, methods to analyze peptides derived from crude protein mixtures and approaches to analyze large numbers of intact proteins by mass spectrometry directly. Examples from this laboratory illustrate biological problem solving by modern mass spectrometric techniques. These include the analysis of the structure and function of the nucleolus and the analysis of signaling complexes.     

Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines

Chromosome‐centric Human Proteome Project aims at identifying and characterizing protein products encoded from all human protein‐coding genes. As of early 2017, 19 837 protein‐coding genes have been annotated in the neXtProt database including 2691 missing proteins that have never been identified by mass spectrometry. Missing proteins may be low abundant in many cell types or expressed only in a few cell types in human body such as sperms in testis. In this study, we performed expression proteomics of two near‐haploid cell types such as HAP1 and KBM‐7 to hunt for missing proteins. Proteomes from the two haploid cell lines were analyzed on an LTQ Orbitrap Velos, producing a total of 200 raw mass spectrometry files. After applying 1% false discovery rates at both levels of peptide‐spectrum matches and proteins, more than 10 000 proteins were identified from HAP1 and KBM‐7, resulting in the identification of nine missing proteins. Next, unmatched spectra were searched against protein databases translated in three frames from noncoding RNAs derived from RNA‐Seq data, resulting in six novel protein‐coding regions after careful manual inspection. This study demonstrates that expression proteomics coupled to proteogenomic analysis can be employed to identify many annotated and unannotated missing proteins.     

Large-scale protein identification using mass spectrometry

Recent achievements in genomics have created an infrastructure of biological information. The enormous success of genomics promptly induced a subsequent explosion in proteomics technology, the emerging science for systematic study of proteins in complexes, organelles, and cells. Proteomics is developing powerful technologies to identify proteins, to map proteomes in cells, to quantify the differential expression of proteins under different states, and to study aspects of protein-protein interaction. The dynamic nature of protein expression, protein interactions, and protein modifications requires measurement as a function of time and cellular state. These types of studies require many measurements and thus high throughput protein identification is essential. This review will discuss aspects of mass spectrometry with emphasis on methods and applications for large-scale protein identification, a fundamental tool for proteomics.     

Trends in mass spectrometry instrumentation for proteomics

Mass spectrometry has become a primary tool for proteomics because of its capabilities for rapid and sensitive protein identification and quantitation. It is now possible to identify thousands of proteins from microgram sample quantities in a single day and to quantify relative protein abundances. However, the need for increased capabilities for proteome measurements is immense and is now driving both new strategies and instrument advances. These developments include those based on integration with multi-dimensional liquid separations and high accuracy mass measurements and promise more than order of magnitude improvements in sensitivity, dynamic range and throughput for proteomic analyses in the near future.     

Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes

We present a large-scale top-down proteomics (TDP) study of plant leaf and chloroplast proteins, achieving the identification of over 4700 unique proteoforms. Using capillary zone electrophoresis coupled with tandem mass spectrometry analysis of offline size-exclusion chromatography fractions, we identify 3198 proteoforms for total leaf and 1836 proteoforms for chloroplast, with 1024 and 363 proteoforms having post-translational modifications, respectively. The electrophoretic mobility prediction of capillary zone electrophoresis allowed us to validate post-translational modifications that impact the charge state such as acetylation and phosphorylation. Identified modifications included Trp (di)oxidation events on six chloroplast proteins that may represent novel targets of singlet oxygen sensing. Furthermore, our TDP data provides direct experimental evidence of the N- and C-terminal residues of numerous mature proteoforms from chloroplast, mitochondria, endoplasmic reticulum, and other sub-cellular localizations. With this information, we suggest true transit peptide cleavage sites and correct sub-cellular localization signal predictions. This large-scale analysis illustrates the power of top-down proteoform identification of post-translational modifications and intact sequences that can benefit our understanding of both the structure and function of hundreds of plant proteins.     

Multivariate approaches in plant science

The objective of proteomics is to get an overview of the proteins expressed at a given point in time in a given tissue and to identify the connection to the biochemical status of that tissue. Therefore sample throughput and analysis time are important issues in proteomics. The concept of proteomics is to encircle the identity of proteins of interest. However, the overall relation between proteins must also be explained. Classical proteomics consist of separation and characterization, based on two-dimensional electrophoresis, trypsin digestion, mass spectrometry and database searching. Characterization includes labor intensive work in order to manage, handle and analyze data. The field of classical proteomics should therefore be extended to also include handling of large datasets in an objective way. The separation obtained by two-dimensional electrophoresis and mass spectrometry gives rise to huge amount of data. We present a multivariate approach to the handling of data in proteomics with the advantage that protein patterns can be spotted at an early stage and consequently the proteins selected for sequencing can be selected intelligently. These methods can also be applied to other data generating protein analysis methods like mass spectrometry and near infrared spectroscopy and examples of application to these techniques are also presented. Multivariate data analysis can unravel complicated data structures and may thereby relieve the characterization phase in classical proteomics. Traditionally statistical methods are not suitable for analysis of the huge amounts of data, where the number of variables exceed the number of objects. Multivariate data analysis, on the other hand, may uncover the hidden structures present in these data. This study takes its starting point in the field of classical proteomics and shows how multivariate data analysis can lead to faster ways of finding interesting proteins. Multivariate analysis has shown interesting results as a supplement to classical proteomics and added a new dimension to the field of proteomics.     

Thylakoid membrane proteomics

Proteomics seeks to monitor the global complement of proteins within a cell or organism and accompanying plasticity with respect to development and environment. The proteome is dynamic, the product of current and past gene expression, countless protein-protein interactions and selective proteolytic systems. Consequently the snapshot that a proteomic measurement yields must be integrated into proteome flux; the flow of nutrients and energy through the protein pathways that catalyze and drive life. The thylakoid membrane proteome poses many technical challenges for proteomics. Integral membrane proteins present awkward physico-chemical properties and the abundant photosynthetic machinery conceals much less abundant and no less important proteins such as channels and transporters that control the interaction of stroma and lumen. Discussed here are contrasting approaches to thylakoid proteomics; 'shotgun' techniques that provide throughput benefits by cleaving proteins into smaller more-manageable peptide chunks versus intact protein techniques that provide more detailed and accurate pictures. A two-dimensional chromatography system directly interfaced to electrospray-ionization mass spectrometry has allowed the direct visualization of large reaction-center proteins (up to 83 kDa) from both Photosystems 1 and 2 providing an attractive avenue for characterization of thylakoid membrane proteomes under different conditions because of the ability to resolve molecular heterogeneity resulting from post-translational modifications such as phosphorylation and oxidation. A high-resolution spectrum of Bacteriorhodopsin recorded to an accuracy of 8 ppm using Fourier-transform mass spectrometry demonstrates the first application of this technique to intact polytopic integral membrane proteins.     

High throughput proteome screening for biomarker detection

Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Current methods, while highly developed and powerful, are falling short of their goal of routinely analyzing whole proteomes mainly because the wealth of proteomic information accumulated from prior studies is not used for the planning or interpretation of present experiments. The consequence of this situation is that in every proteomic experiment the proteome is rediscovered. In this report we describe an approach for quantitative proteomics that builds on the extensive prior knowledge of proteomes and a platform for the implementation of the method. The method is based on the selection and chemical synthesis of isotopically labeled reference peptides that uniquely identify a particular protein and the addition of a panel of such peptides to the sample mixture consisting of tryptic peptides from the proteome in question. The platform consists of a peptide separation module for the generation of ordered peptide arrays from the combined peptide sample on the sample plate of a MALDI mass spectrometer, a high throughput MALDI-TOF/TOF mass spectrometer, and a suite of software tools for the selective analysis of the targeted peptides and the interpretation of the results. Applying the method to the analysis of the human blood serum proteome we demonstrate the feasibility of using mass spectrometry-based proteomics as a high throughput screening technology for the detection and quantification of targeted proteins in a complex system.     

Application of Mass Spectrometry in Proteomics

Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.     

生物质谱在细胞信号转导研究中的应用

近几年快速发展起来的生物质谱技术 ,依靠 (酶解后肽段 )精确质量数测定和随机肽序列标签分析 ,实现了对蛋白质高通量的鉴定 ,并被成功地用于蛋白质相互作用和蛋白质磷酸化等翻译后修饰研究。与传统的研究手段相比 ,上述技术能够在一次实验中对多信号通路中所有磷酸化的蛋白质分子及其磷酸化位点进行鉴定 ,已成为蛋白质组学最新发展中令人关注的一个热点。简要综述质谱技术应用于上述工作中的 3种策略     

利用串联质谱鉴定氨基酸突变的生物信息学算法

氨基酸突变能够改变蛋白的结构和功能,影响生物体的生命过程.基于串联质谱的鸟枪法蛋白质组学是目前大规模研究蛋白质组学的主要方法,但是现有的质谱数据鉴定流程为了提高鉴定结果的灵敏度往往会有意压缩数据库中的氨基酸突变信息.因此,如何挖掘数据中的氨基酸突变信息成为当前质谱数据鉴定的一个重要部分.当前应用于氨基酸突变鉴定的串联质谱鉴定方法大致可以分为3大类:基于序列数据库搜索的方法、基于序列标签搜索的算法以及基于图谱库搜索的算法.本文首先详细介绍了这3种氨基酸突变鉴定算法,并分析了各种方法的特点和不足,然后介绍了氨基酸突变鉴定的研究现状和发展方向.随着基于串联质谱的蛋白质组学的不断发展,蛋白序列中的氨基酸突变信息将被更好地解析出来,从而得以深入探讨由氨基酸突变引起的蛋白结构和功能改变,为揭示氨基酸突变的生物学意义奠定基础.     

What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry

Targeted proteomics has gained significant popularity in mass spectrometry‐based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high‐throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).