Sunday, December 30, 2012

pNOVO+

Another example:pNOVO+ is a new de novo sequencing algorithm that makes use of the complementary fragmentation that we available from HCD and ETD fragmentation.  The authors, Hao Chi  et. al., test their system on peptides derived from a number...
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This month's JPR is awesome!

You're going to be hearing a lot from me about this month's JPR.  Were they saving up all this great stuff for the New Year?  I'm just kind of floored by how many interesting new studies came out all at on...
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Saturday, December 29, 2012

2D isoelectric focusing

This month's JPR includes an article by Maria Pernemalm and Jahnne Lehtio at the Karolinska Institutet.  The subject of the study is a new method for performing 2 dimensional isoelectric focusing.  In the first dimension, proteins are separated...
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Friday, December 28, 2012

Convert ppm to mmu to dalton

Just another little tool that I meant to move over from the old blog. It is a simple Excel sheet to convert PPM for a specific m/z to MMU and to Da.  John Dalton approv...
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Thursday, December 27, 2012

Correlation between iTRAQ reagent sets

A new study in this month's JPR takes a look at the correlation between 2-plex and 6-plex iTRAQ reagent kits. The results are a bit surprising to me, but they two reagent kits show a pretty strong correlation.You can find this study from Rauniyar et....
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Protein Deconvolution Estimator

This is one of those things I posted on the old blog a couple years ago and kept meaning to bring over to this new one.  It is a simple Excel spreadsheet for estimating the deconvoluted mass of an intact protein.  It certainly isn't perfect...
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Wednesday, December 26, 2012

BaseSpace cloud genomics computing

Again, not proteomics.  I may need to re-name this blog soon.  Anyway, BaseSpace cloud genomics is a service from Illumina that is set to kick off in January.  It is an attempt to use brute strength to solve the difficulties of dealing...
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Tuesday, December 25, 2012

Happy Xmas!!! Better top down analysis with ETD

Happy Xmas to my readers who celebrate this holiday.  To my readers who don't, I hope you at least get the day off from work. Short blerb today on an article in this month's issue of MCP.  The study from Fornelli et al., evaluate a new way...
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Monday, December 24, 2012

Papers. A viable alternative to EndNote?

Papers is a program to help us keep track of our citations.  While it is primarily useful for keeping track of literature you have downloaded, it also has handy functions for creating citations in your papers.  At first glance, the $80 price...
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Sunday, December 23, 2012

Targeted quan on a Q Exactive

A new paper in MCP from Gallien et. al., explores the power of the Q Exactive instrument for targeted analysis of proteins and peptides.  The end result:  770 tryptic yeast peptides monitored successfully in a 60 minute gradie...
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Saturday, December 22, 2012

PathCase

PathCase is an NSF funding project at CWRU focusing mapping out biological pathways.  The most unique aspect of this project is the metabolomics analysis workkirunch.  This project is focusing on sorting out the findings of the rapidly growing...
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Friday, December 21, 2012

Delayed fragmentation for improving reporter ions

This article is from 2011, but it had slipped past me until my friend Santosh brought it to my attention recently.  In the study, Savitski, et. al., study the effect of various settings of the chromatography function on an Orbitrap Velos on their...
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Thursday, December 20, 2012

MaxQuant summer school videos

This week, the good people at the Max Planck Institute who gave us MaxQuant released all of their lectures from their summer school series on YouTube.  They are broken into individual lectures of between 40 and 80 minutes each.  You can visit...
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Wednesday, December 19, 2012

Catching up!

I've been having some technical problems lately, primarily relating to my ability to access the internet while on the road.  This hasn't stopped me from typing, however, and I'll be backdating a number of entries that have built up over the last...
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Sunday, December 16, 2012

Tranche! Download proteomic data 1 out of 10 tries.

This is me being overly critical of a service that costs me nothing, right?  The Tranche Proteomics repository at the Proteome Commons is a great idea.  A completely essential idea.  It is awesome that we have it.  But why doesn't...
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Friday, December 14, 2012

Improved chromatography and lower back pressure?

I'm no chromatography expert.  I'm a biologist.  My graduate advisor, however, made chromatograms that would make people at conferences stop in their tracks.  He is just that good (also a biologist...).  I absorbed just enough to...
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Thursday, December 13, 2012

Mass Spectrometry Geekery

I recently stumbled across this page (Mass Spectrometry Geekery) and have revisited a couple of times.  You should definitely check it out. Alex does a great job (definitely better than I'm doing!) of keeping up with the new literature and commenting...
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Wednesday, December 12, 2012

Venny Venn Diagram

A while back I wrote about my favorite Venn Diagram tool.  The Venny Venn Diagram Plotter may actually be better.  It is a freely available, web accessible Venn plotter that will plot your redundancy for you.  For example, if you have...
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Monday, December 10, 2012

iORBI talks for download

Did you miss the 2012 iORBI?Don't despair!  All of the talks presented at all of the iORBI meetings are available for download on Planet Orbitrap.  There are talks on: Tuning and Calibrating your Orbitrap, how best to set up bottom-up and top-down...
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Friday, December 7, 2012

Tabb lab proteomics software

There is a lot of proteomics software out there.  Some good and some...not so good.  But there is just so much now that sometimes really comprehensive and long standing developments will slip right around your notice.  The work of the...
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Wednesday, December 5, 2012

Zwittergent -- another MS compatible detergent

This week I learend about Zwittergent, another MS compatible detergent (like Rapigest and that other thing one I wrote about a while ago).  Zwittergent, however is unique in that it maintains its zwitterionic behavior in solution across a wide pH...
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Monday, December 3, 2012

Measuring Hormones with LC-MS/MS

This week, Dr. Rien Blankenstein will be giving a free talk via webinar on the potential of LC-MS/MS for the measurement of hormone levels. If you are interested in the clinical applications of LC-MS, this talk is probably for you.  For more information,...
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Sunday, December 2, 2012

MS Amanda -- another cool new PD node

Thanks to Santosh for letting me know about this!  MS Amanda is a new high speed scoring node for Proteome Discoverer that is available through pd-nodes.org.  It promises a new and rapid metric and full compatibility with both PD 1.3 and 1.4....
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Saturday, December 1, 2012

Wine Proteomics

I recently wrote about a paper on beer proteomics.  A recent review by Righetti et. al., is a concise and comprehensive overview of the field of wine proteomics.  The review summarizes many of the recent reports on the protein content of wine...
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