scholarly journals Combining Bottom-Up and Top-Down Mass Spectrometric Strategies for De Novo Sequencing of the Crustacean Hyperglycemic Hormone from Cancer borealis

2009 ◽  
Vol 81 (1) ◽  
pp. 240-247 ◽  
Author(s):  
Mingming Ma ◽  
Ruibing Chen ◽  
Ying Ge ◽  
Huan He ◽  
Alan G. Marshall ◽  
...  
Keyword(s):  
De Novo ◽  
De Novo Sequencing ◽  
Mass Spectrometric ◽  
Crustacean Hyperglycemic Hormone ◽  
Top Down ◽  
Cancer Borealis ◽  
Bottom Up ◽  
Hyperglycemic Hormone

scholarly journals De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods

PROTEOMICS ◽  
2017 ◽  
Vol 17 (23-24) ◽  
pp. 1600321 ◽  
Author(s):  
Kira Vyatkina ◽  
Lennard J. M. Dekker ◽  
Si Wu ◽  
Martijn M. VanDuijn ◽  
Xiaowen Liu ◽  
...  
Keyword(s):  
High Resolution ◽  
Mass Spectra ◽  
De Novo ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
Top Down ◽  
Bottom Up ◽  
Tandem Mass Spectra

scholarly journals Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing

2021 ◽  
Vol 22 (11) ◽  
pp. 5476
Author(s):  
Bing Wang ◽  
Zhiwei Wang ◽  
Ni Pan ◽  
Jiangmei Huang ◽  
Cuihong Wan
Keyword(s):  
De Novo ◽  
Average Length ◽  
De Novo Sequencing ◽  
Open Reading Frames ◽  
Start Codon ◽  
Sequence Coverage ◽  
Top Down ◽  
Bottom Up ◽  
Reading Frames ◽  
Small Open Reading Frames

Small open reading frames (sORFs) have translational potential to produce peptides that play essential roles in various biological processes. Nevertheless, many sORF-encoded peptides (SEPs) are still on the prediction level. Here, we construct a strategy to analyze SEPs by combining top-down and de novo sequencing to improve SEP identification and sequence coverage. With de novo sequencing, we identified 1682 peptides mapping to 2544 human sORFs, which were all first characterized in this work. Two-thirds of these new sORFs have reading frame shifts and use a non-ATG start codon. The top-down approach identified 241 human SEPs, with high sequence coverage. The average length of the peptides from the bottom-up database search was 19 amino acids (AA); from de novo sequencing, it was 9 AA; and from the top-down approach, it was 25 AA. The longer peptide positively boosts the sequence coverage, more efficiently distinguishing SEPs from the known gene coding sequence. Top-down has the advantage of identifying peptides with sequential K/R or high K/R content, which is unfavorable in the bottom-up approach. Our method can explore new coding sORFs and obtain highly accurate sequences of their SEPs, which can also benefit future function research.

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra

2015 ◽  
Vol 14 (11) ◽  
pp. 4450-4462 ◽  
Author(s):  
Kira Vyatkina ◽  
Si Wu ◽  
Lennard J. M. Dekker ◽  
Martijn M. VanDuijn ◽  
Xiaowen Liu ◽  
...  
Keyword(s):  
Mass Spectra ◽  
De Novo ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
Top Down ◽  
Tandem Mass Spectra

scholarly journals Top-Down and Bottom-Up Mass Spectrometric Characterization of Human Myoglobin-Centered Free Radicals Induced by Oxidative Damage

2007 ◽  
Vol 79 (16) ◽  
pp. 6236-6248 ◽  
Author(s):  
Leesa J. Deterding ◽  
Suchandra Bhattacharjee ◽  
Dario C. Ramirez ◽  
Ronald P. Mason ◽  
Kenneth B. Tomer
Keyword(s):  
Free Radicals ◽  
Oxidative Damage ◽  
Mass Spectrometric ◽  
Top Down ◽  
Bottom Up ◽  
Human Myoglobin

Combined Top-Down and Bottom-Up Mass Spectrometric Approach to Characterization of Biomarkers for Renal Disease

2005 ◽  
Vol 77 (22) ◽  
pp. 7163-7171 ◽  
Author(s):  
Michael J. Chalmers ◽  
Colin Logan Mackay ◽  
Christopher L. Hendrickson ◽  
Stefan Wittke ◽  
Michael Walden ◽  
...  
Keyword(s):  
Renal Disease ◽  
Mass Spectrometric ◽  
Top Down ◽  
Bottom Up ◽  
Mass Spectrometric Approach

scholarly journals “De-novo” amino acid sequence elucidation of protein G′e by combined “Top-Down” and “Bottom-Up” mass spectrometry

2015 ◽  
Vol 26 (3) ◽  
pp. 482-492 ◽  
Author(s):  
Yelena Yefremova ◽  
Mahmoud Al-Majdoub ◽  
Kwabena F. M. Opuni ◽  
Cornelia Koy ◽  
Weidong Cui ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
De Novo ◽  
Protein G ◽  
Top Down ◽  
Bottom Up

Integrating “Top-Down” and “Bottom-Up” Mass Spectrometric Approaches for Proteomic Analysis ofShewanella oneidensis

2002 ◽  
Vol 1 (3) ◽  
pp. 239-252 ◽  
Author(s):  
Nathan C. VerBerkmoes ◽  
Jonathan L. Bundy ◽  
Loren Hauser ◽  
Keiji G. Asano ◽  
Jane Razumovskaya ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Mass Spectrometric ◽  
Top Down ◽  
Bottom Up

scholarly journals De novo sequencing of proteins and peptides: algorithms, applications, perspectives

2018 ◽  
Vol 1 (1) ◽  
pp. e00005 ◽  
Author(s):  
K.V. Vyatkina
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Database Search ◽  
Mass Spectrometric ◽  
Spectrometric Measurements ◽  
Further Development ◽  
Structure Of Proteins ◽  
Proteins And Peptides

Determination of the primary structure of proteins and peptides constitutes an important step in studying their properties. Currently, mass spectrometry is commonly applied to this end. The results of mass spectrometric measurements can be interpreted by means of either a database search or de novo sequencing methods. The appeal of the latter is due to their applicability to investigating unknown proteins, as well as the ones that cannot be analyzed with genomics or transcriptomics methods. In this paper, we briefly review the existing approaches to de novo sequencing of proteins and peptides, along with the problems that can be solved using those, and indicate directions and perspectives for their further development.

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