scholarly journals Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry

2013 ◽  
Vol 29 (7) ◽  
pp. 821-829 ◽  
Author(s):  
Clement Chung ◽  
Andrew Emili ◽  
Brendan J. Frey
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Bayesian Approach ◽  
Tandem Mass ◽  
Post Translational Modification ◽  
Non Parametric

Data Mining in Protein Identification by Tandem Mass Spectrometry

2011 ◽  
pp. 472-478
Author(s):  
Haipeng Wang
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Tandem Mass Spectrometry ◽  
Large Scale ◽  
Protein Identification ◽  
Peptide Fragmentation ◽  
Tandem Mass ◽  
Fragmentation Pattern ◽  
Post Translational Modification ◽  
Challenges And Opportunities

Protein identification (sequencing) by tandem mass spectrometry is a fundamental technique for proteomics which studies structures and functions of proteins in large scale and acts as a complement to genomics. Analysis and interpretation of vast amounts of spectral data generated in proteomics experiments present unprecedented challenges and opportunities for data mining in areas such as data preprocessing, peptide-spectrum matching, results validation, peptide fragmentation pattern discovery and modeling, and post-translational modification (PTM) analysis. This article introduces the basic concepts and terms of protein identification and briefly reviews the state-of-the-art relevant data mining applications. It also outlines challenges and future potential hot spots in this field.

scholarly journals A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry

2010 ◽  
Vol 9 (5) ◽  
pp. 764-779 ◽  
Author(s):  
Richard C. Baliban ◽  
Peter A. DiMaggio ◽  
Mariana D. Plazas-Mayorca ◽  
Nicolas L. Young ◽  
Benjamin A. Garcia ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Linear Optimization ◽  
Tandem Mass ◽  
Post Translational Modification ◽  
Novel Approach ◽  
Integer Linear Optimization

scholarly journals Global Assessment of Combinatorial Post-translational Modification of Core Histones in Yeast Using Contemporary Mass Spectrometry

2007 ◽  
Vol 282 (38) ◽  
pp. 27923-27934 ◽  
Author(s):  
Lihua Jiang ◽  
Jonell N. Smith ◽  
Shannon L. Anderson ◽  
Ping Ma ◽  
Craig A. Mizzen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Basis Set ◽  
Global Changes ◽  
Tandem Mass ◽  
Wild Type ◽  
Post Translational Modification ◽  
Semiquantitative Assessment ◽  
Core Histones ◽  
Current Mass

A global view of all core histones in yeast is provided by tandem mass spectrometry of intact histones H2A, H2B, H4, and H3. This allowed detailed characterization of >50 distinct histone forms and their semiquantitative assessment in the deletion mutants gcn5Δ, spt7Δ, ahc1Δ, and rtg2Δ, affecting the chromatin remodeling complexes SAGA, SLIK, and ADA. The “top down” mass spectrometry approach detected dramatic decreases in acetylation on H3 and H2B in gcn5Δ cells versus wild type. For H3 in wild type cells, tandem mass spectrometry revealed a direct correlation between increases of Lys4 trimethylation and the 0, 1, 2, and 3 acetylation states of histone H3. The results show a wide swing from 10 to 80% Lys4 trimethylation levels on those H3 tails harboring 0 or 3 acetylations, respectively. Reciprocity between these chromatin marks was apparent, since gcn5Δ cells showed a 30% decrease in trimethylation levels on Lys4 in addition to a decrease of acetylation levels on H3 in bulk chromatin. Deletion of Set1, the Lys4 methyltransferase, was associated with the linked disappearance of both Lys4 methylation and Lys14 and Lys18 or Lys23 acetylation on H3. In sum, we have defined the “basis set” of histone forms present in yeast chromatin using a current mass spectrometric approach that both quickly profiles global changes and directly probes the connectivity of modifications on the same histone.

scholarly journals Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins

2005 ◽  
Vol 16 (12) ◽  
pp. 1985-1999 ◽  
Author(s):  
Judith A. Jebanathirajah ◽  
Jason L. Pittman ◽  
Bruce A. Thomson ◽  
Bogdan A. Budnik ◽  
Parminder Kaur ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Spectrometer ◽  
Tandem Mass ◽  
Post Translational Modification ◽  
Top Down

Online porous graphic carbon chromatography coupled with tandem mass spectrometry for post‐translational modification analysis

2019 ◽  
Vol 33 (15) ◽  
pp. 1240-1247 ◽  
Author(s):  
Rui Chen ◽  
Jacek Stupak ◽  
Sam Williamson ◽  
Susan M. Twine ◽  
Jianjun Li
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Post Translational Modification

scholarly journals Analysis of the Glycan Composition on Plasma Derived ADAMTS13 Employing Tandem Mass Spectrometry

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1069-1069
Author(s):  
Fabian Verbij ◽  
Eva Stokhuijzen ◽  
Floris van Alphen ◽  
Paul Kaijen ◽  
Alexander Meijer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sialic Acid ◽  
Amino Acid ◽  
Tandem Mass Spectrometry ◽  
Consensus Sequence ◽  
Tandem Mass ◽  
Post Translational Modification ◽  
Glycosylation Sites ◽  
High Mannose

Abstract Acquired thrombotic thrombocytopenic purpura (TTP) is a life-threatening disorder that results from the development of auto-antibodies against ADAMTS13 disrupting the binding of ADAMTS13 to von Willebrand factor and thereby preventing the proteinase activity and/or increasing the clearance from the circulation. Previous research from our department identified 9 O-linked glycosylation, 6 O-fucosylation and 2 C-mannosylation sites on plasma derived ADAMTS13. One of the N-linked glycosylation sites (N1354) is close to one of the previously identified peptides preferentially presented on HLA-DRB1*0301 and HLA-DRB1*1501 (ASYILIRD amino acid A1355-D1362) and also close to the HLA-DRB1*1101 peptide (FINVAPHAR amino acid F1328-R1336) suggesting a possible role for the glycosylation in the onset of acquired TTP. To study the glycosylation and glycan trees ADAMTS13 purified from cryosupernatant was reduced with dithiothreitol, alkylated with iodoacetamide and subsequently processed into peptides overnight with either trypsin or chymotrypsin. The peptides were then purified using ZIC-HILIC proteatips and finally analyzed by tandem mass spectrometry employing both higher-energy collision dissociation (HCD) and electron transfer dissociation (ETD). The data files were analyzed using the BYONIC software package as well as manually. Using this approach we identified the glycan structure on 10 N-linked glycosylation. Nine out of 10 glycans contained complex carbohydrate structures terminating in sialic acid. The glycans at these N-linked sites were identified both with or without a fucose on the primary GlcNAc. We were unable to identify a GalNAc residue in the glycan linked to N614 in the spacer domain. This suggest that the glycan on N614 consist primarily of high mannose structures. Binding of ADAMTS13 to the mannose receptor on dendritic cells is most likely facilitated by the high mannose glycan on N614. Furthermore we identified 6 O-linked glycosylation sites either on a serine of a threonine. One O-linked glycan is located in the spacer domain, 2 were found in the thrombospondin type 1 repeat-6 (TSP6), another one was found in TSP8 and 1 O-linked glycosylation site was found in both of the CUB domains. Four out of 6 O-glycans contained terminal sialic acid of which 2 also contained a fucose attached to the GlcNAc. Several O-glycans contained a terminal galactose residue; one O-glycan in TSP6 terminated in both a GlcNAc and a GalNAc residue. O-fucosylation is a common post-translational modification of thrombospondin type 1 repeats. We identified 9 O-fucosylation sites in the TSP repeats. Seven out of 9 sites adhered to the consensus sequence previously defined for O-fucosylation. TSP1 and 2 contained an additional O-fucosylation site at residues T407 and S724; these sites did not match the consensus sequence for O-fucosylation. Interestingly, two additional O-fucosylation sites were identified in cysteine rich and spacer domain at residue S553 and S698. All these residues were predicted to contain a glucose-fucose modification. Next to these glucose-fucose modifications we also identified 2 fucose modification in both of the CUB domains at residues S1170 and T1344. These results show that ADAMTS13 is extensively modified by O-fucosylation. Evidence for C-mannosylation of 8 different tryptophans was obtained. In accordance with previous findings the W387 or W390 (TSP1) and W884 (TSP4) were found to be C-mannosylated. We also found C-mannosylated tryptophans at position and W730 (TSP2) and W1081 (TSP8). Four additional C-mannosylated tryptophans were detected at position W208 (metallo proteinase domain), W1307 (CUB1 domain) and W1379 and W1406 (CUB2 domain). These results show that C-mannosylation is a common post translational modification in ADAMTS13 that is also found outside the TSP domains. Taken together these findings highlight the extensive post translational modification of ADAMTS13 by diverse carbohydrate structures. We anticipate that our findings might be relevant for the clearance and/or immune recognition of ADAMTS13. Disclosures No relevant conflicts of interest to declare.

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