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Topic: Peptide mass fingerprinting

	Oglio Peptide (Site not responding. Last check: 2007-10-08)
		Peptides (like proteins) occur in nature and are responsible for a wide array of functions, many of which are not yetunderstood.
		Antimicrobial peptides generally disrupt the membranes of a target cell, causing lysis of the cell.How this occurs, and what determines the activity and selectivity of these peptides, is currently only known approximately.
		Peptides differ from proteins, which are also long chains of amino acids, byvirtue of their size.
	www.witchware.com /File/14840-Oglio.Peptide.Html (379 words)

	Matrix Science - Help - Accuracy & Resolution
		The presence of isotopes at their natural abundances makes it essential to define whether an experimental mass value is an "average" value, equivalent to taking the centroid of the complete isotopic envelope, or a "monoisotopic" value, the mass of the first peak of the isotope distribution.
		Mass resolution is the dimensionless ratio of the mass of the peak divided by its width.
		To measure a monoisotopic molecular weight requires (i) sufficient mass resolution to resolve the the isotopic distribution (ii) sufficient signal to noise to be able to identify the first peak of the envelope with confidence.
	www.matrixscience.com /help/mass_accuracy_help.html (1055 words)

	Proteome Science \| Full text \| MALDI/MS peptide mass fingerprinting for proteome analysis: identification of ...
		Peptides obtained from protein trypsin digestions may have either hydrophobic or hydrophilic sections, in which case, the direct analysis of such a mixture by MALDI does not allow desorbing of all peptides.
		The peptide mass fingerprint of a protein is believed to be specific enough to identify the protein solely by the comparison of the peptide mass values measured with those calculated by applying the corresponding enzyme cleavage rules, using an appropriate scoring algorithm.
		Monoisotopic peptide masses were matched against the SWISSPROT non-redundant database using 20 or 50 ppm mass tolerance, limited to the Homo Sapiens proteins and with a minimum of matched peptides of 5 (with Protein Prospector).
	www.proteomesci.com /content/1/1/2 (4241 words)

	Peptide mass fingerprinting and amino acid composition identification
		Mass spectrometry is a rapidly growing field of protein analysis, which is proving useful in the identification of proteins separated by 2-D gel electrophoresis.
		This involves the generation of peptides from proteins using residue-specific enzymes, the determination of peptide masses by spectrometric techniques, and the matching of these masses against theoretical peptide libraries generated from protein sequence databases to create a list of likely protein identifications.
		As peptide mass fingerprinting has a sample throughput similar to AA analysis, this combined identification approach is suitable for rapid protein identification.
	us.expasy.org /ch2d/protocols/protocols.fm13.html (287 words)

	[No title] (Site not responding. Last check: 2007-10-08)
		Peptide mass fingerprints can prove as discriminating as linear peptide sequence, but can be obtained in a fraction of the time using less material.
		Peptide mass calculations are based entirely on the linear sequence and use the average isotopic masses of amide-bonded amino acid residues (IUPAC 1987 relative atomic masses).
		Peptide masses can be entered as integers or floating-point values, the latter being rounded to the nearest integer value for the search.
	www.es.embnet.org /Doc/FAQ/MOWSE.html (3411 words)

	Protein Sequencing and Peptide Synthesis Dept (Site not responding. Last check: 2007-10-08)
		Fragment ions mass spectrum corresponds to the sequence of the peptide.
		We perform protein identification by peptide mass fingerprinting on the MALDI-TOF by comparison of the mass profile obtained experimentally with the one obtained theoretically from the proteins in the database.
		In the ion trap, the mass of the intact peptides are measured.
	www.crchul.ulaval.ca /crchul/en/serv/sspeq.asp (1174 words)

	Peptide Mass Fingerprinting an IonSource Tutorial
		Introduction: Peptide Mass Fingerprinting (PMF) is a technique used to identify proteins by matching their constituent fragment masses (peptide masses) to the theoretical peptide masses generated from a protein or DNA database.
		Identification is accomplished by matching the observed peptide masses to the theoretical masses derived from a sequence database.
		In MALDI TOF mass spectrometry, peptides appear as singly charged species in the mass spectrum, see Figure 1, this type of spectrum is simple to interpret unlike an electrospray (ESI) mass spectrum which displays multiply charged species.
	www.ionsource.com /tutorial/protID/fingerprint.htm (833 words)

	PeptideMass - Peptide Characterisation Software
		This program is designed to calculate the theoretical masses of peptides generated by the chemical or enzymatic cleavage of proteins, to assist in the interpretation of peptide mass fingerprinting and peptide mapping experiments.
		Masses have been calculated to 4 or 5 decimal places for all amino acids and post-translational modifications.
		Currently, if there is more than one type of modification in any peptide, a separate mass of the peptide will be given for each type of modification.
	www.expasy.org /tools/peptide-mass-doc.html (2097 words)

	Parasitology: PMF tutorial
		PMF is a method of identifying proteins that relies on the use of a protease to digest the protein in question into a number of smaller peptides.
		The use of the fingerprint to identify proteins is not always possible as it relies on the ability to search data already present in various databases.
		Remember that the sample is being prepared for MS and that relies on accurate mass determination, if you don’t know the exact mass of the cysteines in your peptide, then you cannot accurately predict the mass of peptides that contain a cysteine residue.
	www.aber.ac.uk /parasitology/Proteome/MS_Tut.html (4482 words)

	Peptide mass fingerprinting of chaperonin-containing TCP-1 ( CCT) and copurifying proteins. (Site not responding. Last check: 2007-10-08)
		Peptide mass fingerprinting of chaperonin-containing TCP-1 (CCT) and copurifying proteins.We intend to identify all the other proteins that copurify with CCT and to compile a reference profile for future studies.
		Their identification can be accelerated by a combination of protease digestion, matrix-assisted laser desorption-mass spectrometry, and database matching known as peptide mass fingerprinting.
		We analyzed isoelectric variants of the CCT subunits and differences in the peptide mass spectra of two CCT theta isoforms indicated a novel posttranslational modification of this subunit.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/483323.html (154 words)

	Matrix Science - Help - Peptide Mass Fingerprint
		A mass spectrum of the peptide mixture resulting from the digestion of a protein by an enzyme provides a fingerprint of great specificity.
		However, peptide mass fingerprinting is limited to the identification of proteins for which sequences are already known, it is not a method of structural elucidation.
		The optimum data set for a peptide mass fingerprint is, of course, all of the correct peptides and none of the wrong ones.
	www.matrixscience.com /help/pmf_help.html (865 words)

	High Throughput Peptide Mass Fingerprinting and Protein Macroarray Analysis Using Chemical Printing Strategies -- ...
		Peptide mass analysis data for 14 protein spots are shown in Table I.
		B, the mass spectrum (m/z range of 500 to 1800 Da) of tryptic peptides derived from spot 9 is shown.
		One peptide, m/z 3692.8 Da, was identified as a peptide containing an Asn residue (Asn-83) glycosylated previously based on an increase in m/z of 1.0 Da from the expected peptide mass resulting from the deamidation reaction.
	www.mcponline.org /cgi/content/full/1/7/490 (5317 words)

	Proteomics Core Facility: Peptide mass fingerprinting
		The most common mass spectrometry protein identification technique is called peptide mass fingerprinting.
		This involves the generation of peptides from proteins using trypsin (a specific endoproteolitic enzyme), the determination of peptide masses by spectrometric techniques, and the matching of these masses against theoretical peptide libraries generated from protein sequence databases to create a list of likely protein identifications.
		Experimentally measured, user-specified peptide masses will be compared with the theoretical peptides calculated for all proteins in the Swiss-Prot/TrEMBL databases (Disclaimer).
	tw.expasy.ch /ch2d/service/pmf.html (274 words)

	IN-GEL DIGESTION OF PROTEINS FOR PEPTIDE FINGERPRINT MAPPING (Site not responding. Last check: 2007-10-08)
		Peptide mass fingerprinting uses the peptide masses obtained by digestion to search the protein and DNA databases, to find proteins that show a similar theoretical digest pattern (see eg., Shevchenko et al.
		Generally, trypsin is the protease of choice for peptide mass fingerprinting, because of its reliability and its substrate specificity, yielding peptides with C-terminal basic residues (Arg and Lys), which facilitates ionization and subsequent mass spectrometric sequencing.
		Concentrate the recovered peptides by reducing the final volume of the extracts to ~10 ml in a vacuum centrifuge and add 5 ml 5% Formic acid/ 50% acetonitrile.
	www.bio.vu.nl /vakgroepen/mnb/proteomics/6.in-geldigestion.html (938 words)

	Peptide Mass Fingerprinting
		Peptide mass fingerprinting is a method of identifying a protein by digesting it with an enzyme (trypsin is commonly used) and measuring, by mass spectrometric means, the masses of the peptides produced.
		MALDI (matrix assisted laser desorption/ionization) mass spectrometry is a useful method for analysis because of its sensitivity, higher throughput and slight tolerance for salt in the sample.
		Studies (Speicher, Kaye D., Olivera Kolbas, Sandra Harper and David W. Speicher, “Systematic Analysis of Peptide Recoveries from In-Gel Digestions for Protein Identifications in Proteome Studies” J. Biomolecular Techniques (2000) 11, 74-86) have shown the optimum gel thickness to be 1 mm.
	www.mc.uky.edu /StructuralBiology/PMF_instruct.htm (604 words)

	University of Newcastle Molecular Biology Unit - MASS SPECTROMETRY
		Standard Mass Measurement: This service can provide accurate mass measurement on a range of biomolecules from peptides and nucleotides to lipids, carbohydrates and large proteins.
		Peptide Mass Fingerprint (PMF): Mass fingerprinting of proteins is a technique that uses database searching to identify the parent molecule from the MS spectrum of a digested protein.
		This electrospray instrument is the world's first hybrid triple-stage quadropole / linear ion trap liquid chromatography mass spectrometer for the analysis of biomolecules.
	www.ncl.ac.uk /mbu/pages/ms.htm (227 words)

	UCSF Mass Spectrometry Facility (Site not responding. Last check: 2007-10-08)
		The UCSF Mass Spectrometry Facility, directed by Alma L. Burlingame PhD, is a National Research Resource supported by the National Institutes of Health (grant: NIH NCRR RR01614).
		Our overall purpose is to promote usage of advanced techniques in mass spectrometry by scientists and clinicians in the biomedical community involved in solving problems requiring structural identification at the molecular level.
		The software resources we provide are also mirrored at the UCL-Ludwig Mass Spectrometry Facility (London) and the Joint Protein Structure Laboratory (JSPL) at the Ludwig Institute for Cancer Research (Melbourne Branch).
	donatello.ucsf.edu (250 words)

	MALDI Application Brief - Peptide sequencing strategies (Site not responding. Last check: 2007-10-08)
		Peptides were diluted to a concentration of 20- 50 pmol/ml in H
		Peptide solutions were made to a 1 mg/ml concentration in 0.1% TFA (v/v).
		Acid hydrolysis is particularly advantageous in the instance of peptides blocked at one or both termini, as proteolytic agents such as carboxypeptidase and aminopeptidase are unable to cleave protected termini.
	www.kratos.com /Mapps/NewApps/Apps22.html (1627 words)

	Mapping of proteins in human saliva using two-dimensional gel electrophoresis and peptide mass fingerprinting. (Site not responding. Last check: 2007-10-08)
		Mapping of proteins in human saliva using two-dimensional gel electrophoresis and peptide mass fingerprinting.
		Mapping of proteins in human saliva using two-dimensional gel electrophoresis and peptide mass fingerprinting.One hundred proteins were identified representing 20 different identities according to accession numbers.
		The aim of this work was to map the proteins in saliva by two-dimensional gel electrophoresis (2-DE), and to identify abundant proteins by peptide mass fingerprinting using trypsin cleavage and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry analysis.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/9911531.html (191 words)

	MALDI Application Brief - Peptide sequencing strategies (Site not responding. Last check: 2007-10-08)
		Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) was developed in 1988 to determine the accurate mass of biological and macromolecules to masses in excess of 300 kDa (2,3).
		The mass variation between spectra was most likely due to variations in the distance of the contact lens from the extraction lens of the MALDI system, once clamped onto the target, but could also be due to variation in contact efficiency between the sample and target.
		The less abundant peptides and proteins that are present in reflex tears and also bind to contact lenses, will be further characterized by peptide mass fingerprinting and seamless PSD using the curved field reflectron.
	www.kratos.com /Mapps/NewApps/Apps23.html (1698 words)

	PeptIdent
		PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data.
		Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in the Swiss-Prot/TrEMBL databases.
		When calculating the theoretical peptides from Swiss-Prot, PeptIdent removes signal sequences and/or propeptides (as documented in the Swiss-Prot feature table (FT lines)) before computing pI, Mw and peptide masses for each of the resulting chains.
	www.expasy.ch /tools/peptident.html (398 words)

	Mass Spectrometry (Site not responding. Last check: 2007-10-08)
		Q-TOF Micromass spectrometer, which is an electrospray ionization tandem mass spectrometer containing two different mass analysers, a quadrupole analyser and a Time of Flight analyser and is used for peptide sequencing.
		Sciex API III+ triple quadrupole mass spectrometer (on the right), which is an electrospray ionization tandem mass spectrometer containing three quadrupole mass analysers- (shown with the nano-electrospray interface).
		This instrument is used predominantly for the measurement of protein masses and peptide sequencing applications.
	www.mrc-dunn.cam.ac.uk /facilities/spectrometry.html (109 words)

	ProteinProspector
		MS-Isotope (isotope patterns of peptides and organic molecules)
		Credits: These programs were developed in the UCSF Mass Spectrometry Facility, which is directed by Dr. Alma Burlingame, Professor of
		Clauser K. R., Baker P. and Burlingame A. L., Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.
	prospector.ucsf.edu (234 words)

	MS links, "web diamonds"
		Exact Masses and Isotopic Abundances of the Elements at SIS Table of the elements with exact mass and isotopic distribution.
		Nominal mass determinations, Exact mass (150-1000 Da), High mass accuracy of peptides, ESI of oligonucleotides, ESI of proteins, Multiply charged ions, ESI data on the QTof.
		Middle Atlantic Mass Spectrometry Lab The Johns Hopkins University, Peptides and proteins and post-translation modification, DNA sequencing by MS.
	www.ionsource.com /links/ms_links.htm (2452 words)

	Identification and Phenotypic Characterization of Sphingomonas wittichii Strain RW1 by Peptide Mass Fingerprinting ...
		Identification and Phenotypic Characterization of Sphingomonas wittichii Strain RW1 by Peptide Mass Fingerprinting Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry -- Halden et al.
		Identification and Phenotypic Characterization of Sphingomonas wittichii Strain RW1 by Peptide Mass Fingerprinting Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
		Mass spectrometry is a potentially attractive means of monitoring
	aem.asm.org /cgi/content/abstract/71/5/2442 (336 words)

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