scholarly journals Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data

2011 ◽  
Vol 27 (6) ◽  
pp. 844-852 ◽  
Author(s):  
Stuart R. Jefferys ◽  
Morgan C. Giddings
Keyword(s):  
Mass Spectrometry ◽  
Simulated Annealing ◽  
Mass Spectrometry Data ◽  
Top Down ◽  
Bottom Up ◽  
Post Translational Modifications

scholarly journals Mass spectrometry‐based top‐down and bottom‐up approaches for proteomic analysis of the Moroccan Buthus occitanus scorpion venom

FEBS Open Bio ◽  
2021 ◽  
Author(s):  
Khadija Daoudi ◽  
Christian Malosse ◽  
Ayoub Lafnoune ◽  
Bouchra Darkaoui ◽  
Salma Chakir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Scorpion Venom ◽  
Top Down ◽  
Bottom Up

TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation

2020 ◽  
Author(s):  
In Kwon Choi ◽  
Eroma Abeysinghe ◽  
Eric Coulter ◽  
Suresh Marru ◽  
Marlon Pierce ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Mass Spectrometry Data ◽  
Top Down ◽  
Top Down Mass Spectrometry

scholarly journals VectorMOD: Method for Bottom-Up Proteomic Characterization of rAAV Capsid Post-Translational Modifications and Vector Impurities

2021 ◽  
Vol 12 ◽  
Author(s):  
Neil G. Rumachik ◽  
Stacy A. Malaker ◽  
Nicole K. Paulk
Keyword(s):  
Mass Spectrometry ◽  
Process Development ◽  
Cell Protein ◽  
Macromolecular Complex ◽  
Bottom Up ◽  
Post Translational Modifications ◽  
Simple Step ◽  
Product And Process ◽  
High Doses ◽  
And Control

Progress in recombinant AAV gene therapy product and process development has advanced our understanding of the basic biology of this critical delivery vector. The discovery of rAAV capsid post-translational modifications (PTMs) has spurred interest in the field for detailed rAAV-specific methods for vector lot characterization by mass spectrometry given the unique challenges presented by this viral macromolecular complex. Recent concerns regarding immunogenic responses to systemically administered rAAV at high doses has highlighted the need for investigators to catalog and track potentially immunogenic vector lot components including capsid PTMs and PTMs on host cell protein impurities. Here we present a simple step-by-step guide for academic rAAV laboratories and Chemistry, Manufacturing and Control (CMC) groups in industry to perform an in-house or outsourced bottom-up mass spectrometry workflow to characterize capsid PTMs and process impurities.

Characterization of Human Sperm Protamine Proteoforms through a Combination of Top-Down and Bottom-Up Mass Spectrometry Approaches

2019 ◽  
Vol 19 (1) ◽  
pp. 221-237 ◽  
Author(s):  
Ada Soler-Ventura ◽  
Marina Gay ◽  
Meritxell Jodar ◽  
Mar Vilanova ◽  
Judit Castillo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Sperm ◽  
Top Down ◽  
Bottom Up

scholarly journals Mass graphs and their applications in top-down proteomics

2015 ◽  
Author(s):  
Qiang Kou ◽  
Si Wu ◽  
Nikola Tolić ◽  
Ljiljana Pasa-Tolić ◽  
Xiaowen Liu
Keyword(s):  
Mass Spectrometry ◽  
Early Stage ◽  
Gene Mutations ◽  
Mass Spectrometry Data ◽  
Histone H4 ◽  
Top Down ◽  
Data Set ◽  
Alignment Algorithms ◽  
Protein Functions ◽  
Top Down Mass Spectrometry

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.

Sign in / Sign up

Export Citation Format

Share Document