scholarly journals Calling the Amino Acid Sequence of a Protein/Peptide from the Nanospectrum Produced by a Sub-nanometer Diameter Pore

2021 ◽  
Author(s):  
Xiaowen Liu ◽  
Zhuxin Dong ◽  
Gregory Timp
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Protein Identification ◽  
De Novo ◽  
Protein Sequences ◽  
Protein Molecule ◽  
Thin Membrane ◽  
Computational Tools ◽  
Single Protein ◽  
Extreme Sensitivity

The blockade current that develops when a protein translocates across a thin membrane through a sub-nanometer diameter pore (i.e., a nanospectrum) informs with extreme sensitivity on the sequence of amino acids that constitute the protein. Whereas mass spectrometry (MS) is still the dominant technology for protein identification, it suffers limitations. In proteome-wide studies, MS fails to sequence proteins de novo, but merely classifies a protein and it is not very sensitive requiring about a femtomole to do that. Compared with MS, a sub-nanometer diameter pore (i.e. a sub-nanopore) directly reads the amino acids constituting a single protein molecule, but efficient computational tools are still required for processing and interpreting the blockade current. Here, we delineate computational methods for processing sub-nanopore nanospectra and predicting electrical blockade currents from protein sequences, which are essential for protein identification.

scholarly journals Comparison of Traditional and Industrial Sausages - Baranjski Kulen and Kulenova Seka Using Comprehensive Proteome, Peptidome and Metabolome Techniques

2022 ◽  
Vol 60 (2) ◽  
Author(s):  
Valerija Šimunec ◽  
Rea Bertoša ◽  
Anita Šporec ◽  
Igor Lukić ◽  
Diana Nejašmić ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Volatile Compounds ◽  
Industrial Production ◽  
Free Amino Acids ◽  
Free Amino ◽  
Protein Identification ◽  
Solid Phase ◽  
Gas Chromatography Mass Spectrometry ◽  
Fermented Sausage

Research background. Baranjski kulen is one of the most popular fermented meat sausages originating from Croatia. It has protected geographical indication, and is traditionally produced in the Baranja region of Croatia. Kulenova seka is a fermented sausage very similar to Baranjski kulen, but it has a different caliber and consequently, a shorter time of production. In recent decades, due to the high demand and popularity of these products, industrially produced Baranjski kulen and Kulenova seka have become available on the market. This work aims to identify specific characteristics of traditional and industrial sausages, Baranjski kulen and Kulenova seka on proteome, peptidome and metabolome level which could potentially lead to better optimization of the industrial production process in order to obtain an equivalent to the traditional product. Experimental approach. Protein profiles of Baranjski kulen and Kulenova seka (traditional and industrial) were analysed using two-dimensional gel electrophoresis followed by differential display analysis and protein identification using mass spectrometry. Peptidomics profiling analysis was performed via liquid chromatography-tandem mass spectrometry. Furthermore, aroma profiles were investigated via headspace solid phase microextraction and gas chromatography-mass spectrometry. Results and conclusions. The major identified characteristics of each product were: industrial Baranjski kulen - specific degradation of MYH1 and TITIN, overabundance of stress-related proteins and increased phenylalanine degradation; traditional Baranjski kulen - decreased concentration of phenylalanine and overabundance of ALDOA and CAH3; industrial Kulenova seka - specific MYH4 and HBA degradation process; traditional Kulenova seka - overabundance of DPYD and MYL1, degradation of ALBU and MYG, decreased concentrations of almost all free amino acids and increased amounts of smoke derived volatile compounds. Novelty and scientific contribution. In this preliminary communication, the first insights into protein degradation processes and generation of peptides, free amino acids and aroma compounds of industrial and traditional Baranjski kulen and Kulenova seka are presented. Although further research is needed to draw general conclusions, the specific profile of proteins, peptides, amino acids, and volatile compounds represents the first step in the industrial production of sausages that meet the characteristics of traditional flavour.

Mass spectrometry–based protein identification in proteomics—a review

2020 ◽  
Author(s):  
Zainab Noor ◽  
Seong Beom Ahn ◽  
Mark S Baker ◽  
Shoba Ranganathan ◽  
Abidali Mohamedali
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Comprehensive Analysis ◽  
Pivotal Role ◽  
Computational Tools

Abstract Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.

scholarly journals Metaproteomics approaches and techniques: A review

2017 ◽  
Vol 3 (5) ◽  
pp. 49
Author(s):  
Ayesha Ameen ◽  
Shahid Raza
Keyword(s):  
Mass Spectrometry ◽  
Microbial Community ◽  
Gel Electrophoresis ◽  
Protein Identification ◽  
2D Gel Electrophoresis ◽  
Computational Tools ◽  
2D Gel ◽  
Identification Function ◽  
Related Proteins ◽  
Proteins And Peptides

Extensive studies have been done on metagenomics for various microbial communities. The advancements in metagenomics level led to the need of metaproteomics approaches. Metaproteomics involve the identification, function and expression of various proteins present in microbial community, it also involves the identification and expression analysis of stress related proteins. The concepts of metaproteomics come with advancement in proteomics techniques which includes 2D gel electrophoresis for the identification of proteins and peptides in a particular microbial community. Mass spectrometry which is used to separate the proteins by desorption and ionization using a gas on a liquid medium. MALDI use for protein identification and separation, connected with TOF to give better results. The metaproteomics approaches become more advanced when HPLC and LC were used for peptides and protein with computational tools to sequence the peptide and protein. It is concluded that there is a requirement of research in metaproteomics. Many scientists have done research on these approaches but there is lack of better quality and desirable results.

scholarly journals Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna M. Kotowska ◽  
Gustavo F. Trindade ◽  
Paula M. Mendes ◽  
Philip M. Williams ◽  
Jonathan W. Aylott ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Secondary Ion Mass Spectrometry ◽  
De Novo ◽  
Ion Beam ◽  
Peptide Sequencing ◽  
Protein Characterization ◽  
Label Free ◽  
Peptide Cleavage

AbstractLabel-free protein characterization at surfaces is commonly achieved using digestion and/or matrix application prior to mass spectrometry. We report the assignment of undigested proteins at surfaces in situ using secondary ion mass spectrometry (SIMS). Ballistic fragmentation of proteins induced by a gas cluster ion beam (GCIB) leads to peptide cleavage producing fragments for subsequent OrbitrapTM analysis. In this work we annotate 16 example proteins (up to 272 kDa) by de novo peptide sequencing and illustrate the advantages of this approach by characterizing a protein monolayer biochip and the depth distribution of proteins in human skin.

scholarly journals Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy

2020 ◽  
Vol 21 (8) ◽  
pp. 2870 ◽  
Author(s):  
Irene Malo Estepa ◽  
Haidee Tinning ◽  
Elton Jóse Rosas Vasconcelos ◽  
Beatriz Fernandez-Fuertes ◽  
José María Sánchez ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Protein Synthesis ◽  
Protein Content ◽  
Extracellular Vesicles ◽  
De Novo ◽  
Interferon Tau ◽  
Kunitz Domain ◽  
Pregnancy Recognition ◽  
Domain Protein

Interferon Tau (IFNT), the conceptus-derived pregnancy recognition signal in cattle, significantly modifies the transcriptome of the endometrium. However, the endometrium also responds to IFNT-independent conceptus-derived products. The aim of this study was to determine what proteins are produced by the bovine conceptus that may facilitate the pregnancy recognition process in cattle. We analysed by mass spectrometry the proteins present in conceptus-conditioned media (CCM) after 6 h culture of Day 16 bovine conceptuses (n = 8) in SILAC media (arginine- and lysine-depleted media supplemented with heavy isotopes) and the protein content of extracellular vesicles (EVs) isolated from uterine luminal fluid (ULF) of Day 16 pregnant (n = 7) and cyclic (n = 6) cross-bred heifers on day 16. In total, 11,122 proteins were identified in the CCM. Of these, 5.95% (662) had peptides with heavy labelled amino acids, i.e., de novo synthesised by the conceptuses. None of these proteins were detected in the EVs isolated from ULF. Pregnancy-associated glycoprotein 11, Trophoblast Kunitz domain protein 1 and DExD-Box Helicase 39A were de novo produced and present in the CCM from all conceptuses and in previously published CCM data following 6 and 24 h. A total of 463 proteins were present in the CCM from all the conceptuses in the present study, and after 6 and 24 h culture in a previous study, while expression of their transcripts was not detected in endometrium indicating that they are likely conceptus-derived. Of the proteins present in the EVs, 67 were uniquely identified in ULF from pregnant heifers; 35 of these had been previously reported in CCM from Day 16 conceptuses. This study has narrowed a set of conceptus-derived proteins that may be involved in EV-mediated IFNT-independent embryo–maternal communication during pregnancy recognition in cattle.

AN AUTOMATA APPROACH TO MATCH GAPPED SEQUENCE TAGS AGAINST PROTEIN DATABASE

2005 ◽  
Vol 16 (03) ◽  
pp. 487-497
Author(s):  
YONGHUA HAN ◽  
BIN MA ◽  
KAIZHONG ZHANG
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
De Novo ◽  
De Novo Sequencing ◽  
Computational Method ◽  
Peptide Sequence ◽  
Tandem Mass ◽  
Protein Database ◽  
Matching Algorithm ◽  
Mass Gap

In Biochemistry, tandem mass spectrometry (MS/MS) is the most common method for peptide and protein identifications. One computational method to get a peptide sequence from the MS/MS data is called de novo sequencing, which is becoming more and more important in this area. However De novo sequencing usually can only confidently determine partial sequences, while the undetermined parts are represented by "mass gaps". We call such a partially determined sequence a gapped sequence tag. When a gapped sequence tag is searched in a database for protein identification, the determined parts should match the database sequence exactly, while each mass gap should match a substring of amino acids whose masses add up to the value of the mass gap. In such a case, the standard string matching algorithm does not work any more. In this paper, we present a new efficient algorithm to find the matches of gapped sequence tags in a protein database.

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