Protein de novo sequencing by top-down and middle-down MS/MS: Limitations imposed by mass measurement accuracy and gaps in sequence coverage

2018 ◽  
Vol 427 ◽  
pp. 107-113 ◽  
Author(s):  
Lidong He ◽  
Chad R. Weisbrod ◽  
Alan G. Marshall
Keyword(s):  
Measurement Accuracy ◽  
De Novo ◽  
Mass Measurement ◽  
De Novo Sequencing ◽  
Mass Measurement Accuracy ◽  
Sequence Coverage ◽  
Top Down

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.

High-Mass-Measurement Accuracy and 100 Sequence Coverage of Enzymatically Digested Bovine Serum Albumin from an ESI-FTICR Mass Spectrum

1999 ◽  
Vol 71 (14) ◽  
pp. 2595-2599 ◽  
Author(s):  
James E. Bruce ◽  
Gordon A. Anderson ◽  
Jenny Wen ◽  
Richard Harkewicz ◽  
Richard D. Smith
Keyword(s):  
Mass Spectrum ◽  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Bovine Serum ◽  
Measurement Accuracy ◽  
Mass Measurement ◽  
High Mass ◽  
Mass Measurement Accuracy ◽  
Sequence Coverage

Mass measurement accuracy of the Orbitrap in intact proteome analysis

2016 ◽  
Vol 30 (12) ◽  
pp. 1391-1397 ◽  
Author(s):  
Fan Yu ◽  
Houqin Fang ◽  
Kaijie Xiao ◽  
Yan Liu ◽  
Bingbing Xue ◽  
...  
Keyword(s):  
Measurement Accuracy ◽  
Mass Measurement ◽  
Proteome Analysis ◽  
Mass Measurement Accuracy

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

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry

2005 ◽  
Vol 19 (7) ◽  
pp. 915-918 ◽  
Author(s):  
Adam M. Hawkridge ◽  
Angelito I. Nepomuceno ◽  
Stephanie L. Lovik ◽  
Christopher J. Mason ◽  
David C. Muddiman
Keyword(s):  
Mass Spectrometry ◽  
Fourier Transform ◽  
Cyclotron Resonance ◽  
Measurement Accuracy ◽  
Mass Measurement ◽  
Ion Cyclotron Resonance ◽  
Mass Measurement Accuracy ◽  
Ion Cyclotron

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

Improved protein identification using automated high mass measurement accuracy MALDI FT-ICR MS peptide mass fingerprinting

2004 ◽  
Vol 238 (2) ◽  
pp. 189-196 ◽  
Author(s):  
David M. Horn ◽  
Eric C. Peters ◽  
Heath Klock ◽  
Andrew Meyers ◽  
Ansgar Brock
Keyword(s):  
Protein Identification ◽  
Measurement Accuracy ◽  
Mass Measurement ◽  
Peptide Mass Fingerprinting ◽  
High Mass ◽  
Mass Measurement Accuracy ◽  
Peptide Mass ◽  
Ft Icr Ms ◽  
Ft Icr

Effect of reverse scan on mass measurement accuracy in an ion trap mass spectrometer

2004 ◽  
Vol 39 (6) ◽  
pp. 702-704 ◽  
Author(s):  
Francesco L. Brancia ◽  
Roger Giles ◽  
Li Ding
Keyword(s):  
Mass Spectrometer ◽  
Measurement Accuracy ◽  
Ion Trap ◽  
Mass Measurement ◽  
Mass Measurement Accuracy ◽  
Ion Trap Mass Spectrometer ◽  
Reverse Scan

Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer

2008 ◽  
Vol 22 (10) ◽  
pp. 1563-1566 ◽  
Author(s):  
Michael S. Bereman ◽  
Matthew M. Lyndon ◽  
R. Brent Dixon ◽  
David C. Muddiman
Keyword(s):  
Measurement Accuracy ◽  
Mass Measurement ◽  
Time Of Flight ◽  
Mass Analyzer ◽  
Mass Measurement Accuracy ◽  
Magnetic Sector ◽  
Double Focusing
Sign in / Sign up

Export Citation Format

Share Document