Application of Top-Down Deconvolution Tools to Bottom-Up Mass Spectrometry Data: Advantages and Limitations

Author(s):  
Kirill Tyshuk ◽  
Kira Vyatkina
FEBS Open Bio ◽  
2021 ◽  
Author(s):  
Khadija Daoudi ◽  
Christian Malosse ◽  
Ayoub Lafnoune ◽  
Bouchra Darkaoui ◽  
Salma Chakir ◽  
...  

Author(s):  
In Kwon Choi ◽  
Eroma Abeysinghe ◽  
Eric Coulter ◽  
Suresh Marru ◽  
Marlon Pierce ◽  
...  

2019 ◽  
Vol 19 (1) ◽  
pp. 221-237 ◽  
Author(s):  
Ada Soler-Ventura ◽  
Marina Gay ◽  
Meritxell Jodar ◽  
Mar Vilanova ◽  
Judit Castillo ◽  
...  

2015 ◽  
Author(s):  
Qiang Kou ◽  
Si Wu ◽  
Nikola Tolić ◽  
Ljiljana Pasa-Tolić ◽  
Xiaowen Liu

Although proteomics has made rapid progress in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a "bird view" of intact proteoforms. The combinatorial explosion of possible proteoforms, which may result in billions of possible proteoforms for one protein, makes proteoform identification a challenging computational problem. Here we propose a new data structure, called the mass graph, for efficiently representing proteoforms. In addition, we design mass graph alignment algorithms for proteoform identification by top-down mass spectrometry. Experiments on a histone H4 mass spectrometry data set showed that the proposed methods outperformed MS-Align-E in identifying complex proteoforms.


Radiocarbon ◽  
2021 ◽  
pp. 1-15
Author(s):  
G Salazar ◽  
S Szidat

ABSTRACT Since radiocarbon accelerator mass spectrometry (14C AMS) is considered a high-precision technique, reassessment of the measurement uncertainty has been a topic of interest. Scientists from analytical and metrological fields have developed the top-down and bottom-up measurement of uncertainty approaches. The 14C quoted error should approximate the uncertainty of long-term repetitions of the top-down approach in order to be realistic. The novelty of this paper is that the uncertainty of both approaches were approximated to each other. Furthermore, we apportioned the graphitization, instrumentation, and bias components in order to additively expand the quoted error. Our results are comparable to error multipliers and to long-term repeatability studies reported by other laboratories. Our laboratory was established in late 2012 with N2 as stripper gas and 7 years later, we changed to helium stripper. Thus, we were able to compare both gases, and demonstrate that helium is a better stripper gas. In absolute F14C units, the ranges of graphitization+bias combined uncertainties were (0.7 to 4.1) × 10–3 for N2 and (0.7–3.0) × 10–3 for He depending on the standard 14C content. The error multiplier for He defined as the expanded uncertainty over quoted error, in average, was 1.7; while without the bias, the multiplier was 1.3.


2019 ◽  
Vol 18 (9) ◽  
pp. 3429-3438 ◽  
Author(s):  
Rachel M. Miller ◽  
Robert J. Millikin ◽  
Connor V. Hoffmann ◽  
Stefan K. Solntsev ◽  
Gloria M. Sheynkman ◽  
...  

2017 ◽  
Vol 89 (16) ◽  
pp. 8244-8250 ◽  
Author(s):  
Nobuaki Takemori ◽  
Ayako Takemori ◽  
Piriya Wongkongkathep ◽  
Michael Nshanian ◽  
Rachel R. Ogorzalek Loo ◽  
...  

2015 ◽  
Vol 26 (3) ◽  
pp. 482-492 ◽  
Author(s):  
Yelena Yefremova ◽  
Mahmoud Al-Majdoub ◽  
Kwabena F. M. Opuni ◽  
Cornelia Koy ◽  
Weidong Cui ◽  
...  

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