Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases

Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection

Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized proteomics. Both the resolution of shotgun proteomics methods and the search engines have improved dramatically, allowing for confident identification of SAAV peptides. However, it is not yet known if these methods are truly successful in accurately identifying SAAV peptides without prior genomic information in the search database. We studied this in unprecedented detail by exploiting publicly available long-read RNA sequences and shotgun proteomics data from the gold standard reference cell line NA12878. Searching spectra from this cell line with the state-of-the-art open modification search engine ionbot against carefully curated search databases resulted in 96.7% false-positive SAAVs and an 85% lower true positive rate than searching with peptide search databases that incorporate prior genetic information. While adding genetic variants to the search database remains indispensable for correct peptide identification, inclusion of long-read RNA sequences in the search database contributes only 0.3% new peptide identifications. These findings reveal the differences in SAAV detection that result from various approaches, providing guidance to researchers studying SAAV peptides and developers of peptide spectrum identification tools.

The origin of the expressed retrotransposed gene ACTBL2 and its influence on human melanoma cells' motility and focal adhesion formation

We have recently found that β-actin-like protein 2 (actbl2) forms complexes with gelsolin in human melanoma cells and can polymerize. Phylogenetic and bioinformatic analyses showed that actbl2 has a common origin with two non-muscle actins, which share a separate history from the muscle actins. The actin groups' divergence started at the beginning of vertebrate evolution, and actbl2 actins are characterized by the largest number of non-conserved amino acid substitutions of all actins. We also discovered that ACTBL2 is expressed at a very low level in several melanoma cell lines, but a small subset of cells exhibited a high ACTBL2 expression. We found that clones with knocked-out ACTBL2 (CR-ACTBL2) or overexpressing actbl2 (OE-ACTBL2) differ from control cells in the invasion, focal adhesion formation, and actin polymerization ratio, as well as in the formation of lamellipodia and stress fibers. Thus, we postulate that actbl2 is the seventh actin isoform and is essential for cell motility.

Comparison of different variant sequence types coupled with decoy generation methods used in concatenated target-decoy database searches for proteogenomic research

Concatenated target-decoy database searches are commonly used in proteogenomic research for variant peptide identification. Currently, protein-based and peptide-based sequence databases are applied to store variant sequences for database searches. The protein-based database records a full-length wild-type protein sequence but using the given variant events to replace the original amino acids, whereas the peptide-based database retains only the in silico digested peptides containing the variants. However, the performance of applying various decoy generation methods on the peptide-based variant sequence database is still unclear, compared to the protein-based database. In this paper, we conduct a thorough comparison on target-decoy databases constructed by the above two types of databases coupled with various decoy generation methods for proteogenomic analyses. The results show that for the protein-based variant sequence database, using the reverse or the pseudo reverse method achieves similar performance for variant peptide identification. Furthermore, for the peptide-based database, the pseudo reverse method is more suitable than the widely used reverse method, as shown by identifying 6% more variant PSMs in a HEK293 cell line data set. SIGNIFICANCE: In our survey of publications on proteogenomic studies, 57% of the studies adopt the peptide-based variant sequence database coupled with the reverse method for decoy generation to construct a target-decoy database for searches. However, our results show that when using the peptide-based variant sequence database, it is better to adopt the pseudo reverse method for generating decoy sequences, to avoid leading to fewer variant peptides being identified.

Quantitative Analysis of Antibody Survival across the Infant Digestive Tract Using Mass Spectrometry with Parallel Reaction Monitoring

Orally delivered antibodies may be useful for the prevention of enteric pathogen infection, but to be effective they need to survive intact across digestion through the gastrointestinal tract. As a test case, we fed a recombinant human antibody, palivizumab, spiked into human milk to four infants and collected gastric, intestinal and stool samples. We identified a tryptic peptide from palivizumab (LLIYDTSK) that differs from all endogenous human antibodies and used this for quantitation of the intact palivizumab. To account for dilution by digestive fluids, we co-fed a non-digestible, non-absorbable molecule-polyethylene glycol 28-quantified it in each sample and used this value to normalize the observed palivizumab concentration. The palivizumab peptide, a stable isotope-labeled synthetic peptide and polyethylene glycol 28 were quantified via a highly sensitive and selective parallel-reaction monitoring approach using nano-liquid chromatography/Orbitrap mass spectrometry. On average, the survival of intact palivizumab from the feed to the stomach, upper small intestine and stool were 88.4%, 30.0% and 5.2%, respectively. This approach allowed clear determination of the extent to which palivizumab was degraded within the infant digestive tract. This method can be applied with some modifications to study the digestion of any protein.

SAAVpedia: Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation

Next-generation genome sequencing has enabled the discovery of numerous disease- or drug-response-associated nonsynonymous single nucleotide variants (nsSNVs) that alter the amino acid sequences of a protein. Although several studies have attempted to characterize pathogenic nsSNVs, few have been confirmed as single amino acid variants (SAAVs) at the protein level. Here we developed the SAAVpedia platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. The platform consists of four modules: SAAVidentifier, SAAVannotator, SNV/SAAVretriever, and SAAVvisualizer. The SAAVidentifier provides a reference database containing 18 206 090 SAAVs and performs the identification and quality assessment of SAAVs. The SAAVannotator provides functional annotation with biological, clinical, and pharmacological information for the interpretation of condition-specific SAAVs. The SNV/SAAVretriever module enables bidirectional navigation between relevant SAAVs and nsSNVs with diverse genomic and proteomic data. SAAVvisualizer provides various statistical plots based on functional annotations of detected SAAVs. To demonstrate the utility of SAAVpedia, the proteogenomic pipeline with protein-protein interaction network analysis was applied to proteomic data from breast cancer and glioblastoma patients. We identified 1326 and 12 breast-cancer- and glioblastoma-related genes that contained one or more SAAVs, including BRCA2 and FAM49B, respectively. SAAVpedia is a suitable platform for confirming whether a genomic variant is maintained in an amino acid sequence. Furthermore, as a result of the SAAV discovery of these positive controls, the SAAVpedia could play a key role in the protein functional study for the Human Proteome Project (HPP).

Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine

The increasing availability of high throughput proteomics data provides us with opportunities as well as posing new ethical challenges regarding data privacy and re-identifiability of participants. Moreover, the fact that proteomics represents a level between the genotype and the phenotype further exacerbates the situation, introducing dilemmas related to publicly available data, anonymization, ownership of information and incidental findings. In this paper, we try to differentiate proteomics from genomics data and cover the ethical challenges related to proteomics data sharing. Finally, we give an overview of the proposed solutions and the outlook for future studies.

Proteogenomics in the context of the Human Proteome Project (HPP)

INTRODUCTION

The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue. Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference. Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.

Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry

We performed proteomic analyses of human olfactory epithelial tissue to identify missing proteins using liquid chromatography-tandem mass spectrometry. Using a next-generation proteomic pipeline with a < 1.0% false discovery rate at the peptide and protein levels, we identified 3731 proteins, among which five were missing proteins (P0C7M7, P46721, P59826, Q658L1, and Q8N434). We validated the identified missing proteins using the corresponding synthetic peptides. No olfactory receptor (OR) proteins were detected in olfactory tissue, suggesting that detection of ORs would be very difficult. We also identified 49 and 50 alternative splicing variants mapped at the neXtProt and GENCODE databases, respectively, and 2000 additional single amino acid variants. This data set is available at the ProteomeXchange consortium via PRIDE repository (PXD010025).

Progress and Future Direction of Chromosome-Centric Human Proteome Project

This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HPP NeXt-MP50 Missing Proteins Challenge, authors report 73 missing protein detections that meet the HPP guidelines using several novel approaches. Finally, we discuss future directions.