Protein Discovery has just added six new institutions to the company’s growing list of customer organizations:

• Iwate University
• Okinawa Institute of Science & Technology
• Kyoto University Graduate school of Pharmaceutical Science
• Tokyo University Laboratory for Systems Biology and Medicine
• Children’s Hospital Seattle
• University of Texas Health Science Center at San Antonio

Welcome! We appreciate your business.

Related: Protein Extraction

Plant Physiol Biochem. 2011 Feb 18;
Schacht T, Unger C, Pich A, Wydra K

Polygalacturonases (PGs) of wild-type and non-virulent phenotype conversion mutant (PC) strains of Ralstonia solanacearum were compared by investigating their activities and their inhibition by polygalacturonase-inhibiting proteins (PGIPs) from tomato stems. In cultures of wild-type strain ToUdk2, slimy (s), retarded slimy (rs) and non-slimy (ns) colonies appeared. The conversion of the ‘s’ into the ‘rs’ colony form coincided with the beginning of PG production. PG activity of the PC strain increased about 5 h earlier (at 6 hpi), and was up to 35 times higher in media supplemented with two different tomato stem extracts or polygalacturonic acid, compared to the wild-type at 6 hpi, and generally 4-8 times higher across test media and time. By hydrophobic interaction chromatography (HIC), fluorophor-assisted carbohydrate-polyacrylamid-gel electrophoresis (FACE-PAGE) and mass spectrometry analyses, endo-PG PehA, exo-PGs PehB and PehC were identified. PGs of the PC mutant consisted mainly of endo-PG. The increased PG production after supplementing the medium with tomato cell wall extract was reflected by a higher activity of exo-PGs for both strains. Total PGs (endo-PG and exo-PGs) activities were inhibited by PGIPs of tomato stem extracts. PGIP activity was concentration dependent, constitutively present, and not related to resistance nor susceptibility of tomato recombinant inbred lines to R. solanacearum. The proteinaceous character of the inhibiting component was inferred from ammonium sulphate precipitation. For the first time a plant PGIP activity against a bacterial pathogen is reported. Observations support that endo- and exo-PG synthesis is governed by a sensitive regulatory network, which, in interaction with PGIP and cell wall degradation products, leads to generation or avoidance of elicitor-active oligomers, and, thus, may contribute to the development of the compatible or incompatible interaction.

Endo- and exopolygalacturonases of Ralstonia solanacearum are inhibited by polygalacturonase-inhibiting protein (PGIP) activity in tomato stem extracts.

Looking to save time in the lab? Use Protein Discovery’s FFPE-FASP Protein Digestion Kit to de-paraffinize, un-crosslink, deplete SDS and other contaminants, and digest formalin-fixed paraffin-embedded FFPE tissue samples. Our unique, hot extraction buffer method means incubation takes just 30 minutes — half the time of published protocols!

Download the FFPE-FASP Protein Digestion Kit protocol (pdf).

Protein Discovery’s February 2011 Promotion — Free FASP™ Protein Digestion Kit

Note to our Sample Prep subscribers: Protein Discovery’s February promotion begins today. Purchase any mass spectrometry sample preparation kit or cartridge using our new secure online order form and receive our eight-sample FASP Protein Digestion Kit, free. Protein Discovery has products for protein extraction, solubilization, quantification, fractionation, and digestion, so you’re certain to find something your lab needs right now. Select products using our online order form here.

“The order form was extraordinarily easy to use–way better than phoning or faxing in an order. I also was impressed with how fast the confirmation email came through.” (Jan 6, 2011)

Now That There’s FASP, Everyone’s Going Back to Using SDS

With SDS-containing lysis buffers such as the ones in Protein Discovery’s UPX™ and YPX™ Extraction Kits, you can get unbiased extractions that include even the hard-to-get-at synaptic membrane proteins and completely solubilize the proteome for digestion. Researchers have long known that SDS is best, but the necessary step of removing it prior to digestion used to be a pain. Well, not anymore.

Recent FASP-citing Papers:

• Enhanced Reliability of Avian Influenza Virus (AIV) and Newcastle Disease Virus (NDV) Identification Using Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry (MALDI-MS)
• Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques
• Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

More FASP-citing papers…

Protein Discovery’s FASP Kit is the Simplest, Fastest, Most Convenient, and Least-expensive Way to Use FASP to Deplete Your Sample of SDS and Other Contaminating Species, and Achieve Complete Digestion.

“The FASP Protein Digestion Kit by Protein Discovery has done all the work upfront.  With clear instructions and easy to prepare reagents, this kit has made protein digestion in our lab fast and easy. It is a great value for the time we save.” (Feb 7, 2011)

Protein Discovery’s January 2011 Promotion (is over)

Boston College’s Mass Spectrometry Center Director Marek Domin will very soon be rocking a sweet new 64 GB iPad, thanks to his participation in our January 2011 iPad drawing promotion. Keep reading Sample Prep and follow our twitter feed for the most current information on deals and promotions that can make you happy, or help your lab, or both.

Protein Discovery’s Products for Mass Spectrometry Sample Preparation

UPX™Universal Protein Extraction Kit
YPX™Yeast Protein Extraction Kit
PPS Silent® Surfactant
Proteoloc™ Protease Inhibitor Cocktails
Proteoquant™ Proteome Quantification Assay Kit
Gelfree® 8100 Fractionation System
FASP™ Protein Digestion Kit
FFPE-FASP™ Protein Digestion Kit

Get your order in by February 28, 2011 to receive a free FASP Protein Digestion Kit. Go to Protein Discovery’s product order order form.



As promised, on February 1, Protein Discovery did indeed select the winner of the iPad giveaway event announced in the January edition of their “Sample Prep” newsletter.

In an e-mail to this webmaster, veep Andrea Mravca wrote: “At dinner tonight, we put all the names in a box and had our waiter pick a winner – more old-fashioned than a random number generator!” The winner, a lucky proteome investigator and Protein Discovery product user at Boston College, will soon receive a visit from Protein Discovery’s local rep and a sweet, 64 GB iPad.

Sign up here to receive Protein Discovery’s Sample Prep newsletter and find out about future fun promotions, which will go on all year!

Related: Protein Solubilization

Mol Biosyst. 2010 Apr; 6(4): 677-9
Abe R, Caaveiro JM, Kudou M, Tsumoto K

N-Acylamino acids are a new family of versatile biological surfactants capable of extracting integral membrane proteins of various topologies from the biological membrane, in many instances surpassing the efficiency of commercial detergents.

Solubilization of membrane proteins with novel N-acylamino acid detergents.

Try Our New Order Form for a Chance to Win an iPad

Use our new secure online order form before the end of January, and you’ll automatically be included in our February 1, 2011 iPad giveaway! Choose from any of our sample prep kits and products for protein extraction, quantification, solubilization, fractionation, or FASP digestion. On February 1, we’ll select one of January’s “Ship To” names at random to receive the newest version of Apple’s 64 GB wi-fi enabled iPad.

Protein Discovery’s Product Line-Up at the Start of the Year

After talking with many of you at the ASMS 2010 conference about the art of preparing protein samples for the mass spec, we returned to our laboratories to test a number of new product development concepts. The following new products survived our development and testing processes, and have joined PPS Silent® Surfactant and the Gelfree® 8100 Fractionation System in our product line-up:

UPX™Universal Protein Extraction Kit
Complete Solubilization for Universal Sample Preparation

YPX™Yeast Protein Extraction Kit
Universal Sample Preparation for All Yeasts

Proteoloc™ Protease Inhibitor Cocktails
Protection from Endogenous Proteases During Protein Extraction

Proteoquant™ Proteome Quantification Assay Kit
Accurate BCA Assay Protein Quantification in the Presence of Reducing Agents

FASP™ Protein Digestion Kit
Filter-Aided Sample Prep for Complete Trypsin Digestion

FFPE-FASP™ Protein Digestion Kit (image at right)
Proteome Extraction and Filter-Aided Sample Prep for MS Analysis of FFPE Tissues

All of these new products are very competitively priced and come with our 30-day money-back guarantee. Here’s our new order form. Get your order in by January 31, 2011 to be entered in the February 1 iPad drawing. Good Luck!

Related: FASP Protein Digestion Kit

Lee B, Lopez-Ferrer D, Kim BC, Na HB, Park YI, Weitz KK, Warner MG, Hyeon T, Lee SW, Smith RD, Kim J

Trypsin-coated magnetic nanoparticles (EC-TR/NPs), prepared via a simple multilayer random crosslinking of the trypsin molecules onto magnetic nanoparticles, were highly stable and could be easily captured using a magnet after the digestion was complete. EC-TR/NPs showed a negligible loss of trypsin activity after multiple uses and continuous shaking, whereas the conventional immobilization of covalently attached trypsin on NPs resulted in a rapid inactivation under the same conditions due to the denaturation and autolysis of trypsin. A single model protein, a five-protein mixture, and a whole mouse brain proteome were digested at atmospheric pressure and 37°C for 12 h or in combination with pressure cycling technology at room temperature for 1 min. In all cases, EC-TR/NPs performed equally to or better than free trypsin in terms of both the identified peptide/protein number and the digestion reproducibility. In addition, the concomitant use of EC-TR/NPs and pressure cycling technology resulted in very rapid (∼1 min) and efficient digestions with more reproducible digestion results.

Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles.

Related: Improving Protein Digestion for Shotgun Proteomics, PPS Silent Surfactant

Flaubert Mbeunkui, Michael B. Goshe

To evaluate the implementation of various denaturants and their efficacy in bottom-up membrane proteomic methods using liquid chromatography-mass spectrometry (LC-MS) analysis, microsomes isolated from tomato roots were treated with mass spectrometry-compatible surfactants (RapiGest SF Surfactant from Waters Corporation and PPS Silent Surfactant from Protein Discovery), a chaotropic reagent (guanidine hydrochloride), and an organic solvent (methanol). Peptides were analyzed in triplicate sample and technical replicates by data-independent LC-MS^E analysis. Overall, 2333 unique peptides matching to 662 unique proteins were detected with the order of denaturant method efficacy being RapiGest SF Surfactant, PPS Silent Surfactant, guanidine hydrochloride and methanol. Using bioinformatic analysis, 103 proteins were determined to be integral membrane proteins. When normalizing the data as a percentage of the overall number of peptides and proteins identified for each method, the order for integral membrane protein identification efficacy was methanol, guanidine hydrochloride, RapiGest SF Surfactant, and PPS Silent Surfactant. Interestingly, only 8% of the proteins were identified in all four methods with the silent surfactants having the greatest overlap at 17%. GRAVY analysis at the protein and peptide level indicated that methanol and guanidine hydrochloride promoted detection of hydrophobic proteins and peptides, respectively; however, trypsin activity in the presence of each denaturant was determined as a major factor contributing to peptide identification by LC-MS^E. These results reveal the complementary nature of each denaturant method, which can be used in an integrated approach to provide a more effective bottom-up analysis of membrane proteomes than can be achieved using only a single denaturant.

Investigation of Solubilization and Digestion Methods for Microsomal Membrane Proteome Analysis Using Data-Independent LC-MSE