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SAMPI: Protein Identification with Mass Spectra Alignments

Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker
2007 BMC Bioinformatics  
Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification.  ...  A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database.  ...  The authors want to thank Sven Rahmann for helpful discussions and Martina Mahne for providing the original mass spectrometry data.  ... 
doi:10.1186/1471-2105-8-102 pmid:17386090 pmcid:PMC1851022 fatcat:3nt26ogdovbedlc7vex3ilabhy

Protein Structural Changes During Preparation and Storage of Surimi

Marzieh Moosavi-Nasab, Inteaz Alli, Ashraf A. Ismail, Michael O. Ngadi
2005 Journal of Food Science  
The main chemical components of fish meat are water, crude protein, and lipids, which together make up about 98% of the total mass of the flesh.  ...  The subsequent process is aggregation in which denatured prote in molecules align themselves and interaet with eaeh other at specifie points to form a three dimensional network.  ... 
doi:10.1111/j.1365-2621.2005.tb11467.x fatcat:rnokdfhoenbdpg33shu67u3okq

Gibberellin 2-oxidation and the SLN gene of Pisum sativum

Diane R. Lester, John J. Ross, Jennifer J. Smith, Robert C. Elliott, James B. Reid
1999 The Plant Journal  
Full scan mass spectra were acquired by scanning the range m/z 180 to m/z 600 at 0.8secdecade™ in raw data mode, and enhanced by averaging and background subtraction.  ...  Alignment of the sequences shows some divergence between the two in terms of gaps and residue identity (Figure 2).  ... 
doi:10.1046/j.1365-313x.1999.00501.x pmid:10417727 fatcat:6y4xwn7qzrbnvjcmb4bqhwuyv4


1997 Zenodo  
The FTIR spectra of the extracts were recorded on a Spectra Physics 2000 (Perkin EImer) instrument.  ...  fine mass, or only as coarse fragments.  ...  More recently, a category of Anthrosols was created to cater for soils with profound modification brought about by human actions (FAD-Unesco, 1988) .  ... 
doi:10.5281/zenodo.5516419 fatcat:v2qqsdlu7vglfb6373cgun7jh4

Abstract from the 25th Meeting of the Society for Glycobiology

1997 Glycobiology  
sequence alignment ax ibe hajU for engineering ilfcrnalive llgand specificities Inln rai mannoac-binding protein A (MBP-A) In general.  ...  Ihua removing overlap m t)w 2-1) spectra.  ...  Tha enzyme was purtSed 103-toH and had a native molecular mass of 359 kOa by gal fitrarion.  ... 
doi:10.1093/glycob/7.7.1005 fatcat:74nuukwsb5cg5iadeqctmef2fe

Underwater noise due to precipitation

Lawrence A. Crum, Hugh C. Pumphrey, Andrea Prosperetti, Leif Bjorno
1989 Journal of the Acoustical Society of America  
The many successes of this young science range from the identification and counting of physical and biological inhomogeneities, such as microbubbles, zooplankton, and fish, to the remote sensing of distant  ...  A 3-kHz experimental hybrid transducer with a total length of 18 in. was constructed with a small central mass and two small equal end piston masses.  ...  The sampies included a series of ncoprenes with the same composition except for variable amounts of carbon black filler from 0% to 33%.  ... 
doi:10.1121/1.2026824 fatcat:xbwjl6wggjh5xee7ci2vcphfd4


1956 Clinical Chemistry  
Slonim, (Lynn Hospital, Lynn, Mass.)  ...  After ashing the sampie with alkali at 600° the formed iodide is photometrically determined by its catalytic effect on the reduction of ceric sulphate by arsenic acid.  ... 
doi:10.1093/clinchem/2.4.225 fatcat:uvu65ubgzfez3ddxadfh7u3xii

Relevance of time‐varying properties of the first formant frequency in vowel representation

Maria‐Gabriella Di Benedetto
1985 Journal of the Acoustical Society of America  
Further procedures for identification and characterization of this protein (effect of collagenase, immunoblotting, etc.) are in progress.  ...  We know these two words are synonymous but are not pronounced the same. aligns with/•.b.A.t/but the al cannot be aligned with/m•nt/.  ...  The identification of prominent effects with the elastic waves propagating in the shell will be made.  ... 
doi:10.1121/1.2023018 fatcat:3lbckbce2rglzj7zx3fp4nhiui


1957 Journal of The American Ceramic Society  
—P. compares the use of emission spectra in the X-ray wave-length region, generally excited by fluorescence, with flame spectra in quantitative and qualitative analysis.  ...  carbonic acid-silicic acid complexes which promote the attachment of fibrous protein. 14 references.  ... 
doi:10.1111/j.1151-2916.1957.tb12607.x fatcat:ojda72wxjzb5xdccoq6yqyvv2u

Investigations of an antifungal antibiotic produced by an environmental isolate of Paenibacillus polymyxa

Perrin Hudson Beatty
Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction.  ...  The researchers were interested in whether the mass spectra of the whole bacteria could be used to type pathogenic strains.  ...  in MS spectra of the antifungal material.  ... 
doi:10.7939/r3-mysn-bp93 fatcat:atkvjx2tmrh4phxqbw6tdk4jmm

Correlation Between Gut Microbiota and Depression

Ali Naseribafrouei, Ali Naseribafrouei
2013 unpublished
alignment and trimming Principal component and Evolving Factor Analysis MCR-ALS Resolution of Mixed Spectra Basecalling of resolved Spectra Bacterial Composition Correlation Analysis  ...  Direct sequencing on pool of amplified 16SrRNA gene fragment; resolution of the mixed spectra using MCR-ALS multivariate statistics and taxonomic identification of dominant bacterial components using RDP  ... 

PLO1P regulation of M/G1 transcription in Schizosaccharomyces pombe

Szu Shien Ng
Here, we present evidence that Sep1p interacts with Tdh1p, therefore suggesting a mechanism by which PBF regulates M/G1- specific gene expression, through direct interaction with the RNAP II machinery.  ...  In this thesis, we provide evidence for three transcription factors, Fkh2p, Sep1p and Mbx1p, as components of PBF and describe the isolation a Fkh2p-interacting protein, which we named Lyn1p.  ...  a s s -s p e c tro m e try a n a ly s is Mass spectra were determined in collaboration with Dr. Burch more from Sir Henry Wellcome Functional Genomics Facility, University of Glasgow.  ... 
doi:10.5525/gla.thesis.39023 fatcat:j5wv45s2rbebngpwtx7wjgyrnq

Development of oxidative biosystems for the treatment of industrial coloured wastewaters

Cinzia Pezzella
These sequences, together with the newly isolated laccases, were aligned with ClustalW using default settings for multiple sequence alignments.  ...  Analysis of gene sequences Positions of the ATG start codons and introns in the newly identiWed laccase genes were predicted from conserved intron positions, by alignment of deduced protein sequences with  ...  Appendix This section deals with the work carried out in the Laboratory of BiosCiences at Paul Cezanne University in Marseille, under the supervision of Dr.  ... 
doi:10.6092/unina/fedoa/3391 fatcat:tsn5hdwncvhlveqifqtwswp6sm

Jahrbuch Agrartechnik = Yearbook agricultural engineering Band 17, 2005

:None, Universitätsbibliothek Braunschweig
2005 Jahrbuch Agrartechnik  
Merging single load spectra into representative total load spectra remains an art.  ...  The reduction of the load on the mowers is closely correlated with their mass.  ...  In plant construction, systems for animal housing and animal identification were designed .  ... 
doi:10.24355/dbbs.084-201406201009-0 fatcat:pjcaos36hfg7ngachjubr7cil4

Physiological and molecular aspects of light-regulated development in seedlings [article]

Cindy May Pidgeon, University Of Calgary, University Of Calgary, David M. Reid
Sequences were aligned using ClustalX. The predicted protein sequence and resuiction map %-ere determined using DNA snider.  ...  The predicsed protein is 315 amino acids in length and has a predicted molecular mass of 36.1 kDa which is similar in size to other K C oxiaase enzymes.  ... 
doi:10.11575/prism/18279 fatcat:l2c52f2ty5bvpkmxiucfn2kpgq
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