scholarly journals Uncoiling collagen: a multidimensional mass spectrometry study

The Analyst ◽  
2016 ◽  
Vol 141 (1) ◽  
pp. 157-165 ◽  
Author(s):  
H. J. Simon ◽  
M. A. van Agthoven ◽  
P. Y. Lam ◽  
F. Floris ◽  
L. Chiron ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complex ◽  
Structural Information ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Large Protein ◽  
Tryptic Digest ◽  
Large Protein Complex ◽  
Mass Spectrometry Study ◽  
Multidimensional Mass Spectrometry

Two dimensional mass spectrometry can provide structural information on all peptide ions simultaneously from the tryptic digest of a large protein complex.

scholarly journals Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3728
Author(s):  
Taran Driver ◽  
Nikhil Bachhawat ◽  
Leszek J. Frasinski ◽  
Jonathan P. Marangos ◽  
Vitali Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Finite Mass ◽  
Protein Database ◽  
Spectra Analysis ◽  
Fragment Ions ◽  
Single Precursor ◽  
The Common

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

scholarly journals SmartBac, a new baculovirus system for large protein complex production

2019 ◽  
Vol 1 ◽  
pp. 100003 ◽  
Author(s):  
Yujia Zhai ◽  
Danyang Zhang ◽  
Leiye Yu ◽  
Fang Sun ◽  
Fei Sun
Keyword(s):  
Protein Complex ◽  
Large Protein ◽  
Large Protein Complex ◽  
Baculovirus System

scholarly journals Distinct signalling particles containing ERK/MEK and B-Raf in PC12 cells

2005 ◽  
Vol 387 (1) ◽  
pp. 155-164 ◽  
Author(s):  
Matt MacCORMICK ◽  
Tanja MODERSCHEIM ◽  
Louise W. M. van der SALM ◽  
Anna MOORE ◽  
Shona Clements PRYOR ◽  
...  
Keyword(s):  
Nerve Growth Factor ◽  
Growth Factor ◽  
Pc12 Cells ◽  
Protein Complex ◽  
High Speed ◽  
Velocity Sedimentation ◽  
Large Protein ◽  
Nerve Growth ◽  
Large Protein Complex ◽  
Ionic Detergent

Although several multiprotein complexes containing MAPKs (mitogen-activated protein kinases) have been identified using overexpression of kinases and scaffold proteins, the components of the complexes and their physical properties at endogenous expression levels have not been defined. We characterized a large protein complex containing a nerve-growth-factor-activated ERK (extracellular-signal-regulated kinase) and MEK (MAPK/ERK kinase) in rat pheochromocytoma (PC12) cells. This protein complex fractionated into a high-speed pellet and was resistant to non-ionic detergent treatments that solubilized membranes. Disruption of protein–protein interactions by treatment with high salt was required to facilitate immunoprecipitation of active ERK1 and co-precipitation of MEK1. Microtubule fragments were also present in the detergent-resistant high-speed pellet, and some kinases were bound to them, especially ERK1b (an alternatively spliced isoform of ERK1), which showed a strong preference for binding microtubules. The large protein complex containing ERK1 and MEK1 was resolved by velocity sedimentation from fragments of microtubules; however, it did not contain other scaffolding components known to bind ERK and MEK. B-Raf was also present in a distinct detergent-resistant, microtubule-independent protein complex slightly larger than that containing ERK and MEK. We conclude that there are two independent nerve growth factor-regulated ‘signalling particles’ with an estimated size of 60–75 S, one containing ERK1 and MEK1 and the other containing B-Raf. These signalling particles may have a role in the temporal and spatial regulation of kinase activity inside cells.

Residual counter ions can stabilise a large protein complex in the gas phase

2010 ◽  
Vol 298 (1-3) ◽  
pp. 91-98 ◽  
Author(s):  
Joanna Freeke ◽  
Carol V. Robinson ◽  
Brandon T. Ruotolo
Keyword(s):  
Gas Phase ◽  
Protein Complex ◽  
Large Protein ◽  
Large Protein Complex ◽  
Counter Ions

scholarly journals Reelin molecules assemble together to form a large protein complex, which is inhibited by the function-blocking CR-50 antibody

2000 ◽  
Vol 97 (17) ◽  
pp. 9729-9734 ◽  
Author(s):  
N. Utsunomiya-Tate ◽  
K.-i. Kubo ◽  
S.-i. Tate ◽  
M. Kainosho ◽  
E. Katayama ◽  
...  
Keyword(s):  
Protein Complex ◽  
Large Protein ◽  
Large Protein Complex

Determination of the Interface of a Large Protein Complex by Transferred Cross-saturation Measurements

2002 ◽  
Vol 318 (2) ◽  
pp. 245-249 ◽  
Author(s):  
Tamiji Nakanishi ◽  
Mayumi Miyazawa ◽  
Masayoshi Sakakura ◽  
Hiroaki Terasawa ◽  
Hideo Takahashi ◽  
...  
Keyword(s):  
Protein Complex ◽  
Large Protein ◽  
Large Protein Complex
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