Database Search Engines Research Articles

Mir-675-5p supports hypoxia-induced drug resistance in colorectal cancer cells

BackgroundThe uncontrolled proliferation of cancer cells determines hypoxic conditions within the neoplastic mass with consequent activation of specific molecular pathways that allow cells to survive despite oxygen deprivation. The same molecular pathways are often the cause of chemoresistance. This study aims to investigate the role of the hypoxia-induced miR-675-5p in 5-Fluorouracil (5-FU) resistance on colorectal cancer (CRC) cells.MethodsCRC cell lines were treated with 5-Fu and incubated in normoxic or hypoxic conditions; cell viability has been evaluated by MTT assay. MiR-675-5p levels were analysed by RT-PCR and loss and gain expression of the miRNA has been obtained by the transfection of miRNA antagomir or miRNA mimic. Total protein expression of different apoptotic markers was analysed through western blot assay. MirWalk 2.0 database search engine was used to investigate the putative targets of the miR-675-5p involved in the apoptotic process. Finally, the luciferase assay was done to confirm Caspase-3 as a direct target of the miR-675-5p.ResultsOur data demonstrated that hypoxia-induced miR-675-5p counteracts the apoptotic signal induced by 5-FU, thus taking part in the drug resistance response. We showed that the apoptotic markers, cleaved PARP and cleaved caspase-3, increased combining miR-675-5p inhibition with 5-FU treatment. Moreover, we identified pro-caspase-3 among the targets of the miR-675-5p.ConclusionOur data demonstrate that the inhibition of hypoxia-induced miR-675-5p combined with 5-FU treatment can enhances drug efficacy in both prolonged hypoxia and normoxia, indicating a possible strategy to partially overcome chemoresistance.

Digital Education in Ophthalmology.

Accessibility to the Internet and computer systems has prompted the gravitation towards digital learning in medicine, including ophthalmology. Using the PubMed database and Google search engine, current initiatives in ophthalmology that serve as alternatives to traditional in-person learning with the purpose of enhancing clinical and surgical training were reviewed. This includes the development of teleeducation modules, construction of libraries of clinical and surgical videos, conduction of didactics via video communication, and the implementation of simulators and intelligent tutoring systems into clinical and surgical training programs. In this age of digital communication, teleophthalmology programs, virtual ophthalmological society meetings, and online examinations have become necessary for conducting clinical work and educational training in ophthalmology, especially in light of recent global events that have prevented large gatherings as well as the rural location of various populations. Looking forward, web-based modules and resources, artificial intelligence-based systems, and telemedicine programs will augment current curricula for ophthalmology trainees.

Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator.

Maintaining high sensitivity while limiting false positives is a key challenge in peptide identification from mass spectrometry data. Here, we investigate the effects of integrating the machine learning-based postprocessor Percolator into our spectral library searching tool COSS (CompOmics Spectral library Searching tool). To evaluate the effects of this postprocessing, we have used 40 data sets from 2 different projects and have searched these against the NIST and MassIVE spectral libraries. The searching is carried out using 2 spectral library search tools, COSS and MSPepSearch with and without Percolator postprocessing, and using sequence database search engine MS-GF+ as a baseline comparator. The addition of the Percolator rescoring step to COSS is effective and results in a substantial improvement in sensitivity and specificity of the identifications. COSS is freely available as open source under the permissive Apache2 license, and binaries and source code are found at https://github.com/compomics/COSS.

TIDD: tool-independent and data-dependent machine learning for peptide identification

BackgroundIn shotgun proteomics, database search engines have been developed to assign peptides to tandem mass (MS/MS) spectra and at the same time post-processing (or rescoring) approaches over the search results have been proposed to increase the number of confident peptide identifications. The most popular post-processing approaches such as Percolator and PeptideProphet have improved rates of peptide identifications by combining multiple scores from database search engines while applying machine learning techniques. Existing post-processing approaches, however, are limited when dealing with results from new search engines because their features for machine learning must be optimized specifically for each search engine.ResultsWe propose a universal post-processing tool, called TIDD, which supports confident peptide identifications regardless of the search engine adopted. TIDD can work for any (including newly developed) search engines because it calculates universal features that assess peptide-spectrum match quality while it allows additional features provided by search engines (or users) as well. Even though it relies on universal features independent of search tools, TIDD showed similar or better performance than Percolator in terms of peptide identification. TIDD identified 10.23–38.95% more PSMs than target-decoy estimation for MSFragger, which is not supported by Percolator. TIDD offers an easy-to-use simple graphical user interface for user convenience.ConclusionsTIDD successfully eliminated the requirement for an optimal feature engineering per database search tool, and thus, can be applied directly to any database search results including newly developed ones.

Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes.

Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry (MS) required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post‐translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines – that is, Mascot, Mascot+Percolator, and PEAKS DB – as final identification step, as well as the features of target database on the ability to correctly identify non‐spliced and cis‐spliced peptides. We used ground truth datasets measured by MS to benchmark methods’ performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis‐spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated.

Vascular Dysfunction and Its Cardiovascular Consequences During and After COVID-19 Infection: A Narrative Review.

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV2) has brought out changes in our daily life and has caused severe morbidity and mortality across the globe. Especially, post covid complications may remain a threat to the patient’s life. It may also increase the burden on existing health infrastructure and the country’s economy. This disease affects the respiratory system and other organ systems of the body, such as the cardiovascular system. The aim of the present narrative review is to understand how COVID-19 infection deranges vascular homeostasis, leading to endothelial dysfunction and arterial stiffness in the acute phase and following infection. To this effect, definite keywords were employed to obtain relevant information using PubMed database and Google Scholar search engines. It was documented that preexisting cardiovascular disease enhances morbidity in COVID-19 patients. Moreover, an elevated risk of development of new onset cardiovascular events has also been reported. Even a small amount of myocardial injury was significantly associated with death. The presence of virus in myocardial cells has also been documented. Furthermore, endothelial dysfunction and arterial stiffness were documented in the acute phase and 3–4 weeks to 4 months after COVID infection. The virus enters endothelial cells by binding with ACE2 “receptor” on its surface and deranges cellular machinery. It results in reduced conversion of Ang II to Ang (1–7). Accumulated Ang II then activates PI3K-Akt signaling pathway and regulates endothelial activation and production of IL-6 and reactive oxygen species (ROS). An imbalance between renin angiotensin aldosterone system (RAAS) and kallikrein kinin system (KKS) also occurs, which may cause endothelial dysfunction. It is understandable that the underlying pathophysiology of this altered arterial stiffness is multifactorial, involving various cellular and immunological biomolecules.

345 Development of Breast Disease Teaching in the Low and Lower-Middle Income Countries

AimBreast cancer is the most common cancer worldwide, with incidence and mortality rates significantly worse in the developing world. There is a need to improve general health professional’s knowledge of breast disease. The recent COVID-19 pandemic has led to an increase in use of online resources, and remote teaching has had a significant role in medical education particularly post-pandemic. This project aims to assess available breast disease related online resources for use in the context of medical undergraduate education in low and lower-middle income countries.MethodA search for online resources was conducted using generic search engine and specialist databases. In the planning phase, predefined search terms were selected, and exclusion and inclusion criteria were identified. In the search execution phase resources were searched for, and the main target and resources type were recorded. In the screening and information management phase resources identified were assessed for comprehensiveness using the Royal College of Surgeons Breast learning outcomes.ResultsA total of 33 e-resources were identified that met predefined criteria. This included text-based websites (n = 19), tutorials (n = 8), and video resources (n = 6). The majority of resources were aimed at patients (n = 12). None of the resources identified met all 11 outcomes outlined by the Royal College of Surgeons, however most resources met 10 of the learning objectives (n = 7).ConclusionsThere was a good selection of available educational resources in the area of breast disease, however further exploration of the suitability and usefulness of e-resources in the setting of low and lower-middle income countries is required.

Kidney stone depiction on fictional television: how accurate are they?

Fictional portrayals of medical conditions on television have been shown to significantly shape understanding and management expectations of the viewing public. Given the high prevalence of kidney stone disease, we aimed to assess the frequency of its portrayal on US television and assess whether its depiction was reflective of the current epidemiology or management of urolithiasis in the US. A detailed search was conducted for English language depictions of kidney stones in fictional television using internet, movie and television database search engines. Television episodes with characters depicting a kidney stone occurrence were independently reviewed by two reviewers and analyzed for genre, initial air date on US television, character age, gender, race and management strategy. Seventeen episodes from 13 different television series portrayed a character with a symptomatic kidney stone. The majority were male (88%). Surgical intervention was performed in 7/17 cases (shockwave lithotripsy n = 1, ureteroscopy n = 2, nephrectomy n = 1, transurethral removal n = 1, unknown n = 2), spontaneous passage or medical expulsive therapy in 7/17 cases and no treatment or resolution portrayed in 3/17 cases. The only surgical complication shown was ureteral avulsion during ureteroscopy. Inpatient management was seen in 9/14 (64%) cases with event resolution. This study identified a number of kidney stone depictions that may be misleading or misrepresent the presentation and management of this condition. Although likely portrayed for plot development and dramatic effect, this could potentially reinforce inaccurate beliefs or misconceptions and future depictions should be mindful of this.

Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx.

Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the three-dimensional (3D) structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to noncleavable and MS-cleavable cross-linkers. For both, we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For noncleavable peptides, we implemented a novel dipeptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the dipeptide individually. A posterior error probability (PEP) based on total and partial scores is used to control false discovery rates (FDRs). For MS-cleavable cross-linkers, a score of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace the manual filtering of identifications, which is often necessary when using other pipelines. On benchmark data sets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross-linkers and on a proteome-wide data set of cross-linked Drosophila melanogaster cell lysate. The workflow also supports ion mobility-enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra, and is freely available at https://www.maxquant.org/.

Proteoform Identification and Quantification Using Intact Protein Database Search Engine ProteinGoggle.

Proteomics studies the proteome of organisms, especially proteins that are differentially expressed under certain physiological or pathological conditions; qualitative identification of protein sequences and posttranslational modifications (PTMs) and their positions can help us systematically understand the structure and function of proteoforms. With the development and relative popularity of soft ionization technology (such as electrospray ionization technology) and high mass measurement accuracy and high-resolution mass spectrometers (such as orbitrap), the mass spectrometry (MS) characterization of complete proteins (the so-called top-down proteomics) has become possible and has gradually become popular. Corresponding database search engines and protein identification bioinformatics tools have also been greatly developed. This chapter provides a brief overview of intact protein database search algorithm "isotopic mass-to-charge ratio and envelope fingerprinting" and search engine ProteinGoggle.

Software Measurement by Using Artificial Intelligence

Artificial intelligence (AI) is a subfield of computer science concerned with developing intelligent machines capable of performing tasks similar to those performed by humans. This human‐created intelligence began more than 60 years ago. The goal of previous generations of applications was to demonstrate generic human‐like behaviour. The goal has expanded with the advancement and increased compliance of this technology. It includes areas such as healthcare, gaming, and smart devices. The COVID‐19 epidemic has posed a significant barrier to maintaining a sustainable strategy for mental health support clients with major mental illnesses and clinicians who have had to shift delivery modes quickly. In this study, we have conducted a systematic literature review (SLR) to provide an overview of the current state of the literature related to software measurement of healthcare using artificial intelligence. The study followed a secondary research strategy. The systematic literature review aim was to analyze software measurement of mental health illness in terms of previous literature. This study screened out of 28 research papers out of 1076 initial searches. We used Science Direct, IEEE Xplore, Springer Link, ACM, and Hindawi as database search engines. The research objective was to explore the needs of software applications and automation in the healthcare sector to bring efficiency to the systems. The research concluded that the healthcare setting crucially requires the implementation of software automation.

A Narrative Review of the Risk Factors for Cancer and the Preventive Opportunities: Current Status, Future Perspectives, and Implications for India

Introduction Clinical cancer can arise from heterogenous pathways through various genetic mutations. Although we cannot predict the timeline by which an individual will develop cancer, certain risk assessment tools can be used among high-risk groups for focusing the preventive activities. As primary level of cancer prevention, healthy lifestyle approach is being promoted. The etiological factors for lung cancer include by-products of industrialization and air pollution. We need to factor the increase in household air pollution as well. Methods “PubMed” database and Google search engines were used for searching the relevant articles. Search terms with Boolean operators used include “Cancer prevention,” “Missed opportunities in cancer causation,” and “incidence of risk factors.” This review includes 20 studies and other relevant literature that address the opportunities for cancer prevention. Body The narrative describes the association between many of the risk factors and development of cancer. This includes tobacco, alcohol, infections, air pollution, physical inactivity, diet, obesity, screening and preventive strategies, chemoprevention, biomarkers of carcinogenesis, and factors that prolong the diagnosis of cancer. Discussion Reports from basic science research provide evidence on the potential of biologically active food components and pharmacological agents for mitigating the risk of cancer and its progression. However, some reports from observational studies and randomized trials have been inconsistent. We need to recognize the impact of sociodemographic factors such as age, sex, ethnicity, culture, and comorbid illness on preventive interventions. Spiral computed tomographic scan is a robust tool for early detection of lung cancer. Conclusion Infectious etiology for specific cancers provides opportunities for prevention and treatment. The complex interplay between man and microbial flora needs to be dissected, for understanding the pathogenesis of relevant malignancies. For reducing the morbidity of cancer, we need to focus on prevention as a priority strategy and intervene early during the carcinogenic process.

Efekti vježbi za jačanje mišića poda karlice kod trudnica

The pelvic floor is a complex network formed by deep and superficial muscle structures, the vaginal wall and fascia that provides support to the pelvic organs and maintains continence. Changes in the urinary and muscular system during pregnancy cause pelvic floor muscle dysfunction and stress urinary incontinence (SUI). By strengthening these muscles, the symptoms of incontinence can be alleviated. The aim of this paper is to prove the effectiveness of pelvic floor muscle strengthening exercises in the prevention and treatment of urinary incontinence in pregnant women through a systematic review of the available literature. Using the keywords "pelvic floor exercises", "urinary incontinence", "pregnancy", "prevention", "prenatal period" and "postnatal period", three independent authors searched database search engines (PubMed, Physiotherapy Evidence Database and Cochrane Library) for relevant articles from October 2021 to April 2022 using the predetermined criteria, and selected potential papers. The search resulted in 75 works. The papers older than five years, not available in full text, or not written in English were excluded. Ten works that met the criteria were included in the research. The selection was made by using the Jovell and Navarro-Rubio classification of study designs. The classified papers have provided evidence of the importance of prenatal exercises in improving pelvic floor muscle contractility. Structured, supervised training increases the strength of these muscles, reduces urinary symptoms and incontinence. The exercises to strengthen the muscles of the pelvic floor prevent incontinence, reduce the intensity of symptoms and improve the quality of life during pregnancy and postpartum. Health experts have a significant contribution in the education of pregnant women. It is a priority to develop standardized educational programs through which these exercises will be effectively applied.

The Effect of Extinction Cues on Response Recovery: A Meta-Analysis

A cue presented during Pavlovian extinction may help the recovery of the extinction memory, for which is called an extinction cue (EC). Pavlovian conditioning has been useful as a model of different behavior disorders and extinction as a model for their treatment. Extinguished responses may be recovered under different circumstances, akin to a relapse. Hence, it is important to strengthen extinction memory retrieval. There is contradictory evidence of the effectiveness of ECs to this end. There is also little information about the magnitude of response recovery prevention when using ECs. The magnitude of the ECs effect on response recovery was analyzed by a meta-analysis that considered possible sources of variance in the EC effect. The included studies were gathered mainly through scientific database search engines. Selection criteria included experiments that used a Pavlovian extinction and recovery procedure with an EC test. Effect size was calculated for each relevant experiment. Thirty-seven studies were included. These analyses showed that there is a robust effect of an extinction cue in reducing response recovery, d = 0.71, 95% CI [0.58, 0.85]. This effect is higher when a spontaneous recovery procedure is used and when the experiment is done with non-human animals. Interestingly, the type of control group did not affect the effect size. These results are robust under different statistical analyses, although a publication bias was detected.

The Affecting of Demographic Factors on Utilization of Postpartum Health Service

Background: Based on research states that the prevalence rate of complete postpartum visits (KF) in Indonesia is 37%, where this figure has increased from 2013 of 32.1%. The problem with the achievement of postpartum visits in Indonesia is that the underdeveloped areas mentioned in Presidential Decree Number 63 of 2020, namely North Sumatra, Central Sulawesi, Maluku, Papua and West Papua, occupy the bottom 6 provinces in the complete postnatal visit. The province of West Papua is the region with the lowest KF coverage rate in Indonesia. Subjects and Method: Metaanalysis conducted using the PRISMA systematic guidelines. Population= puerperium mother, Intervention= Urban, Comparison= Rural, Outcome= Utility of postnatal health service. The process of searching for articles was carried out between 2005 and 2021 using a database search engine consisting of; PubMed, Science Direct, Springer Link, and Google Scholar. Based on the database search, there were ten articles that met the criteria with a crosssectional design and observational studies and research that discussed demographic factors (urban & rural) on health care facilities. Results: The results of the analysis had high heterogeneity between studies I2= 94%, so that the Random Effect Model was used. Postnatal mothers living in urban areas increased by 1.48 times in utilizing postnatal care health services compared to postnatal mothers living in rural areas. however it was not statistically significant (SMD= 1.48; 95% CI= 0.90 to 2.44; p= 0.012). Conclusion: Postpartum women who live in urban areas use postpartum health services more than postpartum women who live in rural areas. Keywords: postpartum, postnatal visit, demographic factors Correspondence: Kusmirawati. Masters Program in Public Health, Universitas Sebelas Maret. Jl. Ir. Sutami 36A, Surakarta 57126, Central Java. Email: rendiadiansa@student.uns.ac.id Mobile Number: 08816008735. Journal of Health Policy and Management (2022), 07(03): 176-184 https://doi.org/10.26911/thejhpm.2022.07.03.01

A User Guide to Validation, Annotation, and Evaluation of N-Terminome Datasets with MANTI.

A large variety of enrichment procedures for protein N-termini have been developed to trace protease activity and determine precise cleavage sites, as well as other N-terminal protein modifications. Typically, enriched N-terminal peptides are identified by tandem mass spectrometry using standard database search engines, in many cases the popular MaxQuant software package. MaxQuant Advanced N-termini Interpreter (MANTI) is a software package that helps to validate, annotate, and visualize peptide identifications in N-termini datasets in a rapid and straightforward manner. Usage of MANTI and especially its graphical interface Yoğurtlu MANTI in detail are described to enable users to take full advantage of the software package and the multitude of options it has to offer.

Gingival crevicular fluid alkaline phosphatase activity as growth marker: A systematic review

Background: This review synthesizes the available evidence about the individual skeletal maturity with biological maturity indicators and compares it with the levels of gingival crevicular fluid (GCF) alkaline phosphatase (ALP) activity in growing children. Aims: This systematic review aimed to clarify the question: Is GCF ALP a reliable biomarker to assess skeletal maturity during growth? Objectives: The objective of this systematic review is to collect, compile, and review the existing evidence on the levels of GCF ALP activity in growing children and comparing its reliability with contemporary growth indicators. Materials and Methods: A literature appraisal executed using Entres PubMed, www.ncbi.nim.nih.gov, Scupose, Hinary, Ebsco, Embass, Cochrane; Google Scholar Electronic database search engines were used. The MeSH term used “growth markers in gingival crevicular fluid” or “growth markers in growing children.” Studies published till October, 2020, were included in this study. Data Extraction and Quality Assessment: The data have extracted from the selected articles based on year of publication, study design, age of subjects, instruments used, and author’s conclusions. The quality assessment was executed using BIOCROSS Scale. This scale is exclusive for cross-sectional studies with biomarkers. Results: Literature search identified 731 records from electronic databases and from the partial grey literature (Google scholar) search. Finally, six articles fulfilled eligibility criteria included in the review. Conclusions: All the six studies concluded that GCF ALP activity is a reliable method in determining a skeletal maturity indicator in growing children.

A Study on the Potential Pathways for Existing Drugs against COVID-19

Coronavirus infectious disease 2019 (COVID-19) is a global pandemic declared by the World Health Organization (WHO) in March 2020. This emerging infectious disease is rapidly transmitted and does not only pose a global threat to public health but also badly affects the economy. At present, there is no effective drug to treat COVID-19, leading to a significant challenge upon current global attempts at restraining the outbreak. There are several currently available drugs, also considered as the repurposed drugs are in use for treatment against COVID-19. However, these drugs are not as efficient as it is hoped. Therefore, this study is conducted to further explore into other established antivirus that could function better for COVID-19 treatment. In addition, the pathways that associated with the drugs are identified and potential targeted proteins for the repurposed drugs are also pointed out. The articles for review were selected from several search engine databases, which are ScienceDirect, SpringerLink, PubMed, and Scopus including the keywords COVID-19, SARS, MERS, potential pathways for antiviral drugs as well as repurposed drugs, with more than 50 primary research articles identified. Findings and analysis have discovered potential repurposed drugs that could be used for COVID-19, namely bisoxatin, nitazoxanide and teicoplanin which could be involved in corona-related pathways. Meanwhile, the associated pathways are JAK-STAT, Neprilysin (NEP) and cGAS-STING that counteract excessive immune response and act as a medium for the drugs to access antiviral activities. The repurposed drugs target protein identification is also a critical significance, and it was found that S-protein, TMPRSS2, RdRp and RDB which are the signalling protein can be interrupted by the repurposed drugs, presenting a promising antivirus against SARS-CoV-2. It is concluded that this study will provide information to assist logical design of the repurposed drug for its effectiveness as antivirus against COVID-19

Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS.

Developing a deep and comprehensive understanding of the collection of peptides presented by class I human leukocyte antigens (HLA ), collectively referred to as the immunopeptidome , is conducive to the success of a wide range of immunotherapies. The development of tools that enable the deconvolution of immunopeptidomes in the context of disease can help improve the specificity and effectiveness of therapeutic strategies targeting these peptides, such as adoptive T-cell therapy and vaccines. Here, we describe a computational workflow that facilitates the processing and interpretation of data-independent acquisition mass spectrometry (DIA-MS). We consider a specific variation of DIA-MS known as SWATH-MS. SWATH-MS is a promising technique that can be utilized to reproducibly characterize and quantify immunopeptidomes isolated from a wide range of biological sources. In this workflow, we use an assortment of database search engines and computational tools to build high-quality HLA allele-specific peptide spectral peptide libraries for the analysis of immunopeptidomic datasets acquired by SWATH-MS. Generating and sharing these spectral libraries are essential for the SWATH-MS technology to meet its full potential and to enable the rapid and reproducible quantification of HLA-specific peptides across multiple samples.

Accurate Prediction of Protein Sequences for Proteogenomics Data Integration.

This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.