Mass Spectrometry - Revision history

Xianzhon: /* N-terminal Methionine Cleavage */

2015-10-01T18:29:01Z

N-terminal Methionine Cleavage

← Older revision		Revision as of 18:29, 1 October 2015
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	<br>In summary, N-Met cleavage is:		<br>In summary, N-Met cleavage is:

	*Very likely if the second residue is: A, C, G, or P		*Very likely if the second residue is: A, C, G, P or S
	*Not likely if the second residue is V or T.		*Not likely if the second residue is V or T.
	*There are other more complicated influences from the 3rd and 4th residue.		*There are other more complicated influences from the 3rd and 4th residue.

TheresaRamelot at 15:30, 17 December 2009

2009-12-17T15:30:53Z

← Older revision		Revision as of 15:30, 17 December 2009
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	== '''Compare Mass Spectrometry m/z with Calculated Protein Mass''' ==		== '''Compare Mass Spectrometry m/z with Calculated Protein Mass''' ==

	=== Mass Spectrometry Results from Rutger's University<br> ===		=== Mass Spectrometry Results from Rutger's University<br> ===

	<br>		<br>

	At Rutgers University, spectra are collected on a MALDI-TOF/TOF ([http://cabm-ms.cabm.rutgers.edu/instruments.html ABI-MDS SCIEX 4800]) in single TOF mode.  Samples are prepared by mixing 1 ul of the final protein NMR sample with 10 ul of sinapinic acid (SA) matrix solution<!--StartFragment--> <font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;">(10 mg/ml SA in 50% ACN/50% 0.1% TFA).</span></font>		At Rutgers University, spectra are collected on a MALDI-TOF/TOF ([http://cabm-ms.cabm.rutgers.edu/instruments.html ABI-MDS SCIEX 4800]) in single TOF mode.  Samples are prepared by mixing 1 ul of the final protein NMR sample with 10 ul of sinapinic acid (SA) matrix solution<!--StartFragment--> <font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;">(10 mg/ml SA in 50% ACN/50% 0.1% TFA).</span></font>

	<font face="Verdana, Helvetica, Arial"><~~span style="font-size: 12px;" /~~></font>		<font face="Verdana, Helvetica, Arial"><br></font>

	Results:		Results:

	*The peaks should correspond to your full-length protein mass.		*The peaks should correspond to your full-length protein mass.
	*The red information across the top is the base peak, BP (the peak with the greatest intensity), followed by the intensity		*The red information across the top is the base peak, BP (the peak with the greatest intensity), followed by the intensity
	*The other peaks are typically m/z (mass-to-charge ratio) with z = 2+, 1/2+, 1/3+, etc.~~<font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;" /></font>~~ <!--EndFragment-->		*The other peaks are typically m/z (mass-to-charge ratio) with z = 2+, 1/2+, 1/3+, etc. <!--EndFragment-->

	<br>At Rutger's mass spectrometry data is collected for each NC5 sample, NC sample,and unlabelled sample. Error bars for this measurement are typically < 25 Da, but can be more.		<br>At Rutger's mass spectrometry data is collected for each NC5 sample, NC sample,and unlabelled sample. Error bars for this measurement are typically < 25 Da, but can be more.

TheresaRamelot at 15:30, 17 December 2009

2009-12-17T15:30:09Z

← Older revision		Revision as of 15:30, 17 December 2009
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	== '''Compare Mass Spectrometry m/z with Calculated Protein Mass''' ==		== '''Compare Mass Spectrometry m/z with Calculated Protein Mass''' ==

	=== Mass Spectrometry Results from ~~SPINE~~ ===		=== Mass Spectrometry Results from Rutger's University<br> ===

	<br>~~The mass spectrum chromatogram for many~~ of the ~~purified samples is noted~~ in ~~SPINE~~:		<br>

			At Rutgers University, spectra are collected on a MALDI-TOF/TOF ([http://cabm-ms.cabm.rutgers.edu/instruments.html ABI-MDS SCIEX 4800]) in single TOF mode.  Samples are prepared by mixing 1 ul of the final protein NMR sample with 10 ul of sinapinic acid (SA) matrix solution<!--StartFragment--> <font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;">(10 mg/ml SA in 50% ACN/50% 0.1% TFA).</span></font>

			<font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;" /></font>

			Results:

	*Go to the Purification Batch page from the target page in SPINE for the sample
	*Go to the “Link to Mass Spectrum Image”
	*The peaks should correspond to your full-length protein mass.		*The peaks should correspond to your full-length protein mass.
	*The red information across the top is the base peak, BP (the peak with the greatest intensity), followed by the intensity		*The red information across the top is the base peak, BP (the peak with the greatest intensity), followed by the intensity
	*The other peaks are typically m/z (mass-to-charge ratio) with z = 2+, 1/2+, 1/3+, etc.		*The other peaks are typically m/z (mass-to-charge ratio) with z = 2+, 1/2+, 1/3+, etc.<font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;" /></font> <!--EndFragment-->
	*At Rutgers, spectra are collected on a MALDI-TOF/TOF ([http://cabm-ms.cabm.rutgers.edu/instruments.html ABI-MDS SCIEX 4800]) in single TOF mode.  Samples are prepared by mixing 1 ul of the final protein NMR sample with 10 ul of sinapinic acid (SA) matrix solution <!--StartFragment--><font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;"~~>(10 mg~~/~~ml SA in 50% ACN/50% 0.1% TFA).</span~~></font> <!--EndFragment-->

	<br>~~There will typically be~~ mass spectrometry data for each NC5 sample, NC sample,and unlabelled sample. Error bars for this measurement are typically < 25 Da, but can be more.		<br>At Rutger's mass spectrometry data is collected for each NC5 sample, NC sample,and unlabelled sample. Error bars for this measurement are typically < 25 Da, but can be more.

	<br>Some reasons that the MS mass may not match your calculated mass are:		<br>Some reasons that the MS mass may not match your calculated mass are:

TheresaRamelot: moved MassSpectrometry to Mass Spectrometry

2009-11-11T02:18:30Z

moved MassSpectrometry to Mass Spectrometry

← Older revision	Revision as of 02:18, 11 November 2009
(No difference)

TheresaRamelot at 16:13, 10 November 2009

2009-11-10T16:13:47Z

← Older revision		Revision as of 16:13, 10 November 2009
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	==== References ====		=== References ===

	<references />		<references />

TheresaRamelot at 16:12, 10 November 2009

2009-11-10T16:12:42Z

← Older revision		Revision as of 16:12, 10 November 2009
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	<br>The propensity for cleavage has been analyzed in a 2006 bioinformatics paper by Frottin ''et al.'':<ref>[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]</ref>		<br>The propensity for cleavage has been analyzed in a 2006 bioinformatics paper by Frottin ''et al.'':<ref>[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]</ref>

	~~<br>~~<br>In summary, N-Met cleavage is:		<br>In summary, N-Met cleavage is:

	*Very likely if the second residue is: A, C, G, or P		*Very likely if the second residue is: A, C, G, or P

TheresaRamelot at 16:12, 10 November 2009

2009-11-10T16:12:16Z

← Older revision		Revision as of 16:12, 10 November 2009
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	=== Calculate the expected molecular weight for the NC5 and NC sample ===		=== Calculate the expected molecular weight for the NC5 and NC sample ===

			<br>

	[http://www.scripps.edu/~cdputnam/protcalc.html Protein Calculator] is a nice tool that allows to calculate molecular mass of isotopically labeled proteins		[http://www.scripps.edu/~cdputnam/protcalc.html Protein Calculator] is a nice tool that allows to calculate molecular mass of isotopically labeled proteins

	<br>Another way to calculate the molecular weight for a protein is using the [http://ca.expasy.org/tools/protparam.html ExPASY ProtParam] tool. Just paste your sequence into the web form. The atomic composition at the bottom of the results can be used to correct for the isotopic enrichment as in the examples below.		<br>Another way to calculate the molecular weight for a protein is using the [http://ca.expasy.org/tools/protparam.html ExPASY ProtParam] tool. Just paste your sequence into the web form. The atomic composition at the bottom of the results can be used to correct for the isotopic enrichment as in the examples below.

	=== Examples ===		=== Examples ===

TheresaRamelot at 16:10, 10 November 2009

2009-11-10T16:10:09Z

← Older revision		Revision as of 16:10, 10 November 2009
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	=== N-terminal Methionine Cleavage ===		=== N-terminal Methionine Cleavage ===

	<br>The propensity for cleavage has been analyzed in a ~~recent~~ bioinformatics paper:<ref>[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]</ref>		<br>The propensity for cleavage has been analyzed in a 2006 bioinformatics paper by Frottin ''et al.'':<ref>[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]</ref>

	<br><br>In summary, N-Met cleavage is:		<br><br>In summary, N-Met cleavage is:

TheresaRamelot at 16:09, 10 November 2009

2009-11-10T16:09:10Z

← Older revision		Revision as of 16:09, 10 November 2009
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	==== References ====		==== References ====

			<references />
	<references />

	~~[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]~~

TheresaRamelot at 16:08, 10 November 2009

2009-11-10T16:08:18Z

← Older revision		Revision as of 16:08, 10 November 2009
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	=== N-terminal Methionine Cleavage ===		=== N-terminal Methionine Cleavage ===

	<br>The propensity for cleavage has been analyzed in a recent bioinformatics paper:<ref>F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49</ref>		<br>The propensity for cleavage has been analyzed in a recent bioinformatics paper:<ref>[http://www.ncbi.nlm.nih.gov/pubmed/16963780?dopt=Abstract F. Frottin, A. Martinez, P. Peynott, M. Sanghamitra, R. C. Holz, C. Giglione, T. Meinnel, Mol Cell Proteomics, 2006, 5, 2336-49]</ref>

	<br><br>In summary, N-Met cleavage is:		<br><br>In summary, N-Met cleavage is: