scholarly journals Tandem Mass Spectrum Identification via Cascaded Search

2015 ◽  
Vol 14 (8) ◽  
pp. 3027-3038 ◽  
Author(s):  
Attila Kertesz-Farkas ◽  
Uri Keich ◽  
William Stafford Noble
Keyword(s):  
Mass Spectrum ◽  
Tandem Mass Spectrum ◽  
Tandem Mass

scholarly journals The Linoleic Acid Content of the Stratum Corneum of Ichthyotic Golden Retriever Dogs Is Reduced as Compared to Healthy Dogs and a Significant Part Is Oxidized in Both Free and Esterified Forms

Metabolites ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 803
Author(s):  
Iuliana Popa ◽  
Audrey Solgadi ◽  
Didier Pin ◽  
Adrian L. Watson ◽  
Marek Haftek ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Linoleic Acid ◽  
Mass Spectrum ◽  
Stratum Corneum ◽  
Electrospray Ionization ◽  
Tandem Mass Spectrum ◽  
Octadecadienoic Acid ◽  
Free Form ◽  
Tandem Mass

Golden Retrievers may suffer from Pnpl1-related inherited ichthyosis. Our study shows that in the stratum corneum (SC) of ichthyotic dogs, linoleic acid (LA) is also present in the form of 9-keto-octadecadienoic acid (9-KODE) instead of the acylacid form as in normal dogs. The fatty acids purified from SC strips (LA, acylacids) were characterized by liquid chromatography-tandem mass spectrometry (LC-MS) and atmospheric pressure chemical ionization (APCI). Electrospray ionization (ESI) and MS2(MS/MS Tandem mass spectrum/spectra)/M3 (MS/MS/MS Tandem mass spectrum/spectra) fragmentation indicated the positions of the double bonds in 9-KODE. We showed that ichthyotic dogs have a threefold lower LA content in the form of acylacids. The MS2 fragmentation of acyl acids showed in some peaks the presenceof an ion at the m/z 279, instead of an ion at m/z 293 which is characteristic of LA. The detected variant was identified upon MS3 fragmentation as 9-keto-octadecadienoic acid (9-KODE), and the level of this keto-derivative was increased in ichthyotic dogs. We showed by the APCI that such keto forms of LA are produced from hydroperoxy-octadecadienoic acids (HpODE) upon dehydration. In conclusion, the free form of 9-KODE was detected in ichthyotic SC up to fivefold as compared to unaffected dogs, and analyses by HPLC (High performance liquid chromatography) and ESI-MS (Electrospray Ionization-Mass Spectrometry) indicated its production via dehydration of native 9-HpODE.

scholarly journals Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

2016 ◽  
Author(s):  
Fengchao Yu ◽  
Ning Li ◽  
Weichuan Yu
Keyword(s):  
Mass Spectrum ◽  
Computational Complexity ◽  
Large Scale ◽  
Tandem Mass Spectrum ◽  
State Of The Art ◽  
Score Function ◽  
Identification Problem ◽  
Cross Linking ◽  
Tandem Mass ◽  
Data Set

AbstractChemical cross-linking coupled with mass spectrometry is a powerful tool to study protein-protein interactions and protein conformations. Two linked peptides are ionized and fragmented to produce a tandem mass spectrum. In such an experiment, a tandem mass spectrum contains ions from two peptides. The peptide identification problem becomes a peptide-peptide pair identification problem. Currently, most existing tools don’t search all possible pairs due to the quadratic time complexity. Consequently, a significant percentage of linked peptides are missed. In our earlier work, we developed a tool named ECL to search all pairs of peptides exhaustively. While ECL does not miss any linked peptides, it is very slow due to the quadratic computational complexity, especially when the database is large. Furthermore, ECL uses a score function without statistical calibration, while researchers1,2 have demonstrated that using a statistical calibrated score function can achieve a higher sensitivity than using an uncalibrated one.Here, we propose an advanced version of ECL, named ECL 2.0. It achieves a linear time and space complexity by taking advantage of the additive property of a score function. It can analyze a typical data set containing tens of thousands of spectra using a large-scale database containing thousands of proteins in a few hours. Comparison with other five state-of-the-art tools shows that ECL 2.0 is much faster than pLink, StavroX, ProteinProspector, and ECL. Kojak is the only one tool that is faster than ECL 2.0. But Kojak does not exhaustively search all possible peptide pairs. We also adopt an e-value estimation method to calibrate the original score. Comparison shows that ECL 2.0 has the highest sensitivity among the state-of-the-art tools. The experiment using a large-scale in vivo cross-linking data set demonstrates that ECL 2.0 is the only tool that can find PSMs passing the false discovery rate threshold. The result illustrates that exhaustive search and well calibrated score function are useful to find PSMs from a huge search space.

scholarly journals OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Yaojun Wang ◽  
Fei Yang ◽  
Peng Wu ◽  
Dongbo Bu ◽  
Shiwei Sun
Keyword(s):  
Mass Spectrum ◽  
Open Source ◽  
Open Source Software ◽  
Tandem Mass Spectrum ◽  
Tandem Mass ◽  
Spectrum Prediction
Sign in / Sign up

Export Citation Format

Share Document