Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.

Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and noncleavable cross-linked peptides in MS data. MetaMorpheusXL identifies MS-cleavable cross-linked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared with similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable cross-linkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXL compared with programs such as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable cross-link search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.

Molecular ion index assisted comprehensive profiling of B-type oligomeric proanthocyanidins in rhubarb by high performance liquid chromatography-tandem mass spectrometry.

Proanthocyanidins (PAs) are major anti-diarrhea constituents in rhubarb, one of the frequently used traditional medicines. However, the phytochemical investigation of PAs in rhubarb was hampered by their strenuous purification and identification. In the present study, aiming to clarify the distribution of PAs in different rhubarb species, a molecular ion index was priorly established according to the structural features of B-type PAs, which led to a series of targeted discovery of oligomeric PAs in rhubarb by the HPLC-ESI-MS/MS method. Totally, 66 oligomeric PAs including 27 dimers, 29 trimers, and 10 tetramers were tentatively identified on the basis of their MS/MS spectra from 28 rhubarb samples derived from 5 Rheum species as R. palmatum, R. tanguticum, R. officinale, R. coreanum, and R. laciniatum. It is noteworthy that 6 propelargonidins, 14 prodelphinidins, and 10 procyanidin-tetramers were identified from rhubarb for the first time. The profiling comparison of these oligomeric PAs in different rhubarb samples was achieved by visualizing their abundance in a heat map, which indicated the dominant PAs in rhubarb were procyanidin-dimer and its galloylated derivatives.

Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics.

pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data.

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.

Evaluating and mapping of spatial air ion quality patterns in a residential garden using a geostatistic method.

Negative air ions (NAI) produce biochemical reactions that increase the levels of the mood chemical serotonin in the environment. Moreover, they benefit both the psychological well being and the human body's physiological condition. The aim of this research was to estimate and measure the spatial distributions of negative and positive air ions in a residential garden in central Taiwan. Negative and positive air ions were measured at thirty monitoring locations in the study garden from July 2009 to June 2010. Moreover, Kriging was applied to estimate the spatial distribution of negative and positive air ions, as well as the air ion index in the study area. The measurement results showed that the numbers of NAI and PAI differed greatly during the four seasons, the highest and the lowest negative and positive air ion concentrations were found in the summer and winter, respectively. Moreover, temperature was positively affected negative air ions concentration. No matter what temperature is, the ranges of variogram in NAI/PAI were similar during four seasons. It indicated that spatial patterns of NAI/PAI were independent of the seasons and depended on garden elements and configuration, thus the NAP/PAI was a good estimate of the air quality regarding air ions. Kriging maps depicted that the highest negative and positive air ion concentration was next to the waterfall, whereas the lowest air ions areas were next to the exits of the garden. The results reveal that waterscapes are a source of negative and positive air ions, and that plants and green space are a minor source of negative air ions in the study garden. Moreover, temperature and humidity are positively and negatively affected negative air ions concentration, respectively. The proposed monitoring and mapping approach provides a way to effectively assess the patterns of negative and positive air ions in future landscape design projects.