Eric Hill

37 Questions 22 Answers 0 Followers

Questions related from Eric Hill

What is the exact meaning of realative protein abundance(a.u) in LFQ?

I quantified creatine kinase protein in two different samples then I got a bar graph shows a higher number of relative protein abundance in Sample 1 compared to sample 2. My question what this...

25 January 2017 8,620 2 View

Whats the mean of protein quantification by (MaxLFQ) with minimum ratio count of two unique peptides?

In Protein quantification by (MaxLFQ) with minimum ratio count of two unique peptides was setup,is the criteria of quantification depends on the presence of these 2 unique peptides in Protein A in...

23 January 2017 2,431 2 View

What is the differences between bottom-up and top-down proteomics approach?

Its general questions also about the quality of results between the two methods?what about the total protein ID?for example if I performed the two methods for 2 protein mixtures, in one of the...

18 January 2017 3,741 3 View

Why there is a difference between ms/ms m/z for specific peptide and its ms m/z?

I looked to excel file results from MaxQuant, and I noticed for example in one protein a list of peptides, when I checked the value of ms m/z it was 840.05 and of ms ms m/z value it was 840.35 why...

22 August 2016 5,584 6 View

Can creatine kinase M-type protein(43 kDa) be separated in 2DE in around 39 kDa?

I separated proteins from porcine muscle tissue, and I noticed that three spots from CK-m type protein were resolved in around 39 kDa. My question is there any species or modified form of this...

11 July 2016 10,009 3 View

Is protein concentration using Amicon Ultra spin column, consider as protein precipitation step?

I had my protein sample in 8M urea, and I sent my samples to another lab to perform 2DE. The people there only concentrated the sample using 10 KDa Amicon Ultra spin column, does this step...

30 June 2016 4,878 2 View

How I can calculate the number of oxidation peptides properly from the proteome discoverer list?

I tried to calculate the total number of oxidation peptides but I noticed that on the list same oxidation peptides were given twice or even the third time for the same peptide.What does this...

09 May 2016 953 2 View

Can anybody suggest me good paper or review regarding proteolysis in sample preparation in proteomics and action of proteases?

I'm searching for good papers and reviews talk about the proteolytic degradation of proteins by the action of proteases during sample preparation in proteomics for mass spec measurement.Nice...

10 March 2016 6,195 1 View

Does a high concentration of DTT (1M) any serious and significant effect on protein separation in SDS-PAGE?

I used on my protein extract from a tissue a high concentration of DTT(1M), I faced a problem because of this high concentration in protein quantification because all the methods have interfered...

05 January 2016 7,116 9 View

How can we explain the difference in lane intensity in SDS-PAGE after loading the same amount of protein in two lanes?

I performed SDS-PAGE and load the same amount of protein (30 ug) from the same tissue, but with different extraction procedure. One lane is more intense than the other and looks that I load more...

29 December 2015 8,609 7 View

Could an mzXML file work on proteome discoverer 2.0 and MaxQuant 1.5.2.8 ?

I performed my analysis on QTOF Premier(Micromass, Waters),then I converted my raw data file by proteinlynx Global server 2.5.2 to mzxML file.I would like to use this mzXML file in proteome...

26 November 2015 5,318 2 View

What is the degree of proteases action on sample?

I checked the degree of proteases actions on protein samples by performed SDS-PAGE from muscle tissue sample,i loaded the sample on 4 different incubation time at RT without using any...

12 June 2015 335 4 View

Could I lose many of my proteins in around 9ml PBS solution?

I keep my protein in solution of 6.5 ml of 1x PBS from invitrogen plus 0.5 ml water,so i have 7ml protein solution in PBS and water ,i kept this solution at -80c for further...

30 April 2015 6,883 3 View

How can i measure protein concentration by nanodrop if these proteins are in 6M urea?

I have protein extracts in 6M urea with protease inhibitors and i plan to perform protein concentration by nanodrop.And my second question is it useful to use protease inhibitors in such solution?

29 April 2015 9,206 8 View

What are the reasons behind the identified low number of proteins by Orbitarp Fusion?

I measured tryptic peptides from my pocrine tissue samples and I was able to identify only 100 proteins from whole sds-page!! I used sus scrofa database (could this be the reason?) or the kind of...

24 February 2015 2,362 1 View

How we can fix this problem in safety cabinet?

A larm message appeared on the screen of our safety cabinet: incorrect laminar flow. The problem that we don't have manual for this, and the company did not exist anymore. Any suggestions from...

17 February 2015 2,120 2 View

Why do some of protein molecular weights identified with LC-MS/MS not correlated to molecular weights measured on SDS-PAGE ?

I performed SDS-PAGE from tissue extracts then i cut some bands,digested them,then injected to LC-MS/MS.I noticed from the results that most of the molecular weight of identified proteins are not...

08 January 2015 2,075 4 View

What are the optimum parameters for sonicate protein extraction without affecting on protein samples?

I have protein extraction from mamalian tissue,I want to do sonication to get rid of DNA and RNA then I will measure protein concentration by using nanodrop,and finally I will run on SDS-PAGE. I'm...

07 October 2014 800 10 View

Could anybody provide me with the written SOP for Waters Micromass Q-Tof Premier Mass Spectrometer?

Recently, I started working on Q-TOF. I faced a problem in sequential steps to run samples and wonder if the run of GluFib is OK or not. Therefore, I'm looking for a written SOP for Waters...

10 September 2014 6,883 5 View

Could anybody suggest a lysis buffer that compatible with mass spectrometry analysis?

I would like to extract proteins from mamalian muscle tissues,run 2DE then apply the desired digested spots to mass spectrometry,therefore im looking for a lysis buffer for these kinds of tissue...

21 August 2014 4,351 6 View

What is the optimum concentration of protease inhibitor cocktail that i must add to protein extraction from mamalian tissue?

I have a frozen tube of protein extraction from 1 cm2 of bovine muscle,i want to add a protease inhibitor cocktail to this tube without thawing the protein. I had stock solution from inhibitor...

17 July 2014 5,250 4 View

Can anybody help me color the 2DE spots?

I performed 2DE for 4 samples and got 4 gels. I tried to color the spots in these different gels using photoshop cc software, but I could not save the colored file later. Can anyone help me color...

20 May 2014 7,652 3 View

I performed four 2de gels and I want to compare these patterns. I want to color these spots using GIMP 2.8 software. How can I do this?

How can I color the spots using GIMP 2.8 software? I used the program but I can only change the background. I could not color the spots.

11 May 2014 7,769 2 View

Can anybody explain to me what could be the reasons that I could not find any differences in spots between the four gel patterns?

I performed 2DE from cancer cell line. I had 4 gels, one with control, other are treated with anti-cancer drug with 3 different incubation time but I could not find any differences between the...

06 May 2014 9,065 10 View

Can anybody suggest a good and easy free-software for 2DE interpretation and result?

I have four patterns of 2DE gels from my cell lysate and I want to compare these patterns using software. I tried before with the naked eye and but it was too difficult.

23 April 2014 9,992 4 View

Which is the most convenient method for dissolving dried protein in 6 M urea or water?

I would like to prepare casein as standard protein for mass spectrometry analysis. I weighed 1 mg and I need to dissolve it to be ready for tryptic digestion. But I am confused which solution...

22 April 2014 8,817 3 View

Which is better: MTT or cell viability assay?

I would like to determine the concentration of an anti-cancer drug on a cancer cell line to determine the concentration that I have to use to kill only half of the cells. I used a cell viability...

22 April 2014 5,222 23 View

Can anybody explain to me why the result from BCA protein estimation is not correct between different dilutions?

I performed protein estimation using BCA FROM thermo-scientific,i did dilution 1:10,1:100,1:1000. i noticed that the three results after i multiply by dilution factor is very far from each...

16 April 2014 424 2 View

Are the number of passages (age of cancer cells) important?

I'm working on cancer cell lines to get a general overview about proteome and phosphoproteome, and identify the proteins. I reached passage number 35 on my cell till. My question is: Are the...

15 April 2014 1,249 1 View

Can anybody explain to me why I did these steps in my interpretation of SCX-TiO2 results?

I'm interpreting my SCX-TiO2 results and am looking for the amount of glutamate and aspartate in the peptide sequences. I'm looking for the phosphopeptides that are diluted in different fractions...

07 April 2014 5,141 1 View

Can anybody provide me with a manual (not readymade kit) protocol for TiO2 enrichment for phosphopeptides?

I have my own optimized protocol for standard protein using 1 pmol, but I need a suitable protocol for my protein extraction with amount 2 mg of protein.

28 November 2013 3,810 8 View

What is the suitable concentration of phosphatse and phosphorylase inhibitors which I have to use in my lysis buffer?

I need to prepare 8 M urea as lysis buffer to extract the proteins from cancer cell lines. Therefore I 'd like to know what suitable amount of cocktail inhibitors shall I use?

23 November 2013 1,693 1 View

For cancer cell lines, is there any passage limit number at which I must stop splitting my cells, or because it's cancerous cells it's not affected?

I've reached now passage number 50 and I want to extract the protein for proteomics study

01 November 2013 4,023 0 View

What is the best concentration and incubation time for Bortezomib on myeolama cell lines to study its effect on as much protein as possible?

And any papers to support this?

11 October 2013 8,151 1 View

I have lysed my cells by 8 M urea, but I could not take supernatent well due to high viscous of pellet - can anyone help?

I have lysed my cells using 8 M urea, but I noticed that the pellet is very viscous and it was hard to get rid of pellet and take supernatent. Why did this happened? and is it affected on measure...

24 September 2013 7,734 6 View

Did anybody try FK-2 ubiquitin antibody? Howdoes it work with WB and immunoprecipitation?

Did anybody try FK-2 ubiquitin antibody?How its work with WB and immunoprecipitation?

16 September 2013 5,671 1 View

Can anybody suggest a cell lysis buffer suitable for mass spec?

I am searching for a protein lysis buffer for human cancer cells that is compatabile with mass spec. analysis.I have used RIPA buffer but the people from the mass spec facility told me, that the...

15 September 2013 6,079 4 View