Pretreatment of Mass Spectral Profiles:  Application to Proteomic Data

2007 ◽  
Vol 79 (18) ◽  
pp. 7014-7026 ◽  
Author(s):  
Reidar Arneberg ◽  
Tarja Rajalahti ◽  
Kristian Flikka ◽  
Frode S. Berven ◽  
Ann C. Kroksveen ◽  
...  
Keyword(s):  
Mass Spectral ◽  
Proteomic Data ◽  
Spectral Profiles

scholarly journals Mass spectral characterization of primary emissions and implications in source apportionment of organic aerosol

2020 ◽  
Vol 13 (6) ◽  
pp. 3205-3219 ◽  
Author(s):  
Weiqi Xu ◽  
Yao He ◽  
Yanmei Qiu ◽  
Chun Chen ◽  
Conghui Xie ◽  
...  
Keyword(s):  
Source Apportionment ◽  
Spectral Characteristics ◽  
Organic Aerosol ◽  
Water Soluble ◽  
Spectral Characterization ◽  
Rural Site ◽  
Spectral Features ◽  
Mass Spectral ◽  
Spectral Profiles ◽  
Primary Emissions

Abstract. Source apportionment of organic aerosol (OA) from aerosol mass spectrometer (AMS) or aerosol chemical speciation monitor (ACSM) measurements relies largely upon mass spectral profiles from different source emissions. However, the changes in mass spectra of primary emissions from AMS–ACSM with the newly developed capture vaporizer (CV) are poorly understood. Here we conducted 21 cooking, crop straw, wood, and coal burning experiments to characterize the mass spectral features of OA and water-soluble OA (WSOA) using SV-AMS and CV-ACSM. Our results show overall similar spectral characteristics between SV-AMS and CV-ACSM for different primary emissions despite additional thermal decomposition in CV, and the previous spectral features for diagnostics of primary OA factors are generally well retained. However, the mass spectral differences between OA and WSOA can be substantial for both SV-AMS and CV-ACSM. The changes in f55 (fraction of m∕z 55 in OA) vs. f57, f44 vs. f60, and f44 vs. f43 in CV-ACSM are also observed, yet the evolving trends are similar to those of SV-AMS. By applying the source spectral profiles to a winter CV-ACSM study at a highly polluted rural site in the North China Plain, the source apportionment of primary OA was much improved, highlighting the two most important primary sources of biomass burning and coal combustion (32 % and 21 %). Considering the rapidly increasing deployments of CV-ACSM and WSOA studies worldwide, the mass spectral characterization has significant implications by providing essential constraints for more accurate source apportionment and making better strategies for air pollution control in regions with diverse primary emissions.

scholarly journals Correlation between Phylogroups and Intracellular Proteomes ofPropionibacterium acnesand Differences in the Protein Expression Profiles between Anaerobically and Aerobically Grown Cells

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Itaru Dekio ◽  
Renata Culak ◽  
Min Fang ◽  
Graham Ball ◽  
Saheer Gharbia ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Opportunistic Pathogen ◽  
Growth Conditions ◽  
Culture Conditions ◽  
Type I ◽  
Proteomic Data ◽  
Spectral Profiles ◽  
Group B ◽  
Protein Expression Profiles

Propionibacterium acnesis one of the dominant commensals on the human skin and also an opportunistic pathogen in relation to acne, sarcoidosis, prostate cancer, and various infections. Recent investigations using housekeeping and virulence genes have revealed that the species consists of three major evolutionary clades (types I, II, and III). In order to investigate protein expression differences between these phylogroups, proteomic profiles of 21 strains ofP. acneswere investigated. The proteins extracted from cells cultured under anaerobic and aerobic conditions were analysed using a SELDI-TOF mass spectrometer, high-resolution capillary gel electrophoresis, and LC-MS/ MS. The SELDI spectral profiles were visualised as a heat map and a dendrogram, which resulted in four proteomic groups. Strains belonging to type I were represented in the proteome Group A, while Group B contained type III strains. Groups C and D contained mixtures of types I and II. Each of these groups was not influenced by differences in culture conditions. Under anoxic growth conditions, a type IB strain yielded high expressions of some proteins, such as methylmalonyl-CoA epimerase and the Christie-Atkins-Munch-Petersen (CAMP) factor. The present study revealed good congruence between genomic and proteomic data suggesting that the microenvironment of each subtype may influence protein expression.

Alignment of DNA Mass-Spectral Profiles Using Network Flows

2013 ◽  
pp. 149-160
Author(s):  
Pavel Skums ◽  
Olga Glebova ◽  
Alex Zelikovsky ◽  
Zoya Dimitrova ◽  
David Stiven Campo Rendon ◽  
...  
Keyword(s):  
Network Flows ◽  
Mass Spectral ◽  
Spectral Profiles

scholarly journals Cyclohexane Carboxylate and Benzoate Formation from Crotonate in Syntrophus aciditrophicus

2006 ◽  
Vol 73 (3) ◽  
pp. 930-938 ◽  
Author(s):  
Housna Mouttaki ◽  
Mark A. Nanny ◽  
Michael J. McInerney
Keyword(s):  
Sodium Bicarbonate ◽  
Pure Culture ◽  
Carbon Skeleton ◽  
Mass Unit ◽  
Mass Spectral ◽  
Cyclohexane Carboxylate ◽  
Spectral Profiles ◽  
Syntrophus Aciditrophicus ◽  
Derivatives Of ◽  
Tms Derivatives

ABSTRACT The anaerobic, syntrophic bacterium Syntrophus aciditrophicus grown in pure culture produced 1.4 � 0.24 mol of acetate and 0.16 � 0.02 mol of cyclohexane carboxylate per mole of crotonate metabolized. [U-13C]crotonate was metabolized to [1,2-13C]acetate and [1,2,3,4,5,7-13C]cyclohexane carboxylate. Cultures grown with unlabeled crotonate and [13C]sodium bicarbonate formed [6-13C]cyclohexane carboxylate. Trimethylsilyl (TMS) derivatives of cyclohexane carboxylate, cyclohex-1-ene carboxylate, benzoate, pimelate, glutarate, 3-hydroxybutyrate, and acetoacetate were detected as intermediates by comparison of retention times and mass spectral profiles to authentic standards. With [U-13C]crotonate, the m/z-15 ion of TMS-derivatized glutarate, 3-hydroxybutyrate, and acetoacetate each increased by +4 mass units, and the m/z-15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +6 mass units. With [13C]sodium bicarbonate and unlabeled crotonate, the m/z-15 ion of TMS derivatives of glutarate, pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +1 mass unit, suggesting that carboxylation occurred after the synthesis of a four-carbon intermediate. With [1,2-13C]acetate and unlabeled crotonate, the m/z-15 ion of TMS-derivatized 3-hydroxybutyrate, acetoacetate, and glutarate each increased by +0, +2, and +4 mass units, respectively, and the m/z-15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, cyclohexane carboxylate, and 2-hydroxycyclohexane carboxylate each increased by +0, +2, +4, and +6 mass units. The data are consistent with a pathway for cyclohexane carboxylate formation involving the condensation of two-carbon units derived from crotonate degradation with CO2 addition, rather than the use of the intact four-carbon skeleton of crotonate.

Biomarker discovery in mass spectral profiles by means of selectivity ratio plot

2009 ◽  
Vol 95 (1) ◽  
pp. 35-48 ◽  
Author(s):  
Tarja Rajalahti ◽  
Reidar Arneberg ◽  
Frode S. Berven ◽  
Kjell-Morten Myhr ◽  
Rune J. Ulvik ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Selectivity Ratio ◽  
Mass Spectral ◽  
Spectral Profiles

scholarly journals Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data

2003 ◽  
Vol 2003 (5) ◽  
pp. 308-314 ◽  
Author(s):  
Antonia Vlahou ◽  
John O. Schorge ◽  
Betsy W. Gregory ◽  
Robert L. Coleman
Keyword(s):  
Ovarian Cancer ◽  
Decision Tree ◽  
Regression Tree ◽  
Classification And Regression Tree ◽  
Mass Spectral ◽  
Protein Mass ◽  
Proteomic Data ◽  
Decision Tree Classification ◽  
Seldi Proteinchip

Recent reports from our laboratory and others support the SELDI ProteinChip technology as a potential clinical diagnostic tool when combined withn-dimensional analyses algorithms. The objective of this study was to determine if the commercially available classification algorithm biomarker patterns software (BPS), which is based on a classification and regression tree (CART), would be effective in discriminating ovarian cancer from benign diseases and healthy controls. Serum protein mass spectrum profiles from 139 patients with either ovarian cancer, benign pelvic diseases, or healthy women were analyzed using the BPS software. A decision tree, using five protein peaks resulted in an accuracy of 81.5% in the cross-validation analysis and 80%in a blinded set of samples in differentiating the ovarian cancer from the control groups. The potential, advantages, and drawbacks of the BPS system as a bioinformatic tool for the analysis of the SELDI high-dimensional proteomic data are discussed.

scholarly journals Gas Chromatography-Mass Spectrometry Profiles of Ten Pilea Species (Urticaceae)

2016 ◽  
Vol 20 (2) ◽  
pp. 10
Author(s):  
José Hipólito Isaza Martínez ◽  
Ana Julia Colmenares ◽  
Victor Manuel Pineda Orozco ◽  
Ana Isabel Vásquez V.
Keyword(s):  
Gas Chromatography ◽  
Field Trips ◽  
Ethyl Esters ◽  
Gas Chromatography Mass Spectrometry ◽  
Methyl Ethyl ◽  
Mass Spectral ◽  
Large Size ◽  
Spectral Profiles ◽  
Valle Del Cauca ◽  
Made In

The genus Pilea Lindley is the largest among the Urticaceae family. The large size and little commercial interest of this genus make difficult its taxonomy, with few revisions since Weddell.Very few revisions have been reported about the Colombian species since 1939, when Killip made a contribution to the genus for the northern Andes (Ecuador, Peru, Colombia, and Venezuela). To contribute to the knowledge of the Pilea genus in Colombia, field trips were made in the department of Valle del Cauca and ten herbarium samples were analyzed using gas chromatography-mass spectral profiles analysis; which allowed us to identify 33 compounds type monoterpene, sesquiterpene,diterpene, free fatty acids or their methyl, ethyl esters or amides, and triterpenes. It was concluded that Triterpenes were the best chemotaxonomical discriminants for the ten herbarium samples as ten species.

Biomarker discovery from mass spectral profiles: A combined proteomics and multivariate analysis

2008 ◽  
Vol 34 (1) ◽  
pp. S27
Author(s):  
Tarja Rajalahti ◽  
R. Arneberg ◽  
F.S. Berven ◽  
A.C. Kroksveen ◽  
M. Berle ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Biomarker Discovery ◽  
Mass Spectral ◽  
Spectral Profiles
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