Mohsen Sohrabi

22 Questions 20 Answers 0 Followers

Questions related from Mohsen Sohrabi

Which primer do you recomend for saliva microbiome profiling? Which one can give me more data on bacterial species level?

I will sequence my samples on illumina Illumina MiSeq (paired-end). The candidate primers are: 926F/1392R (V6-V8) 803F/1392R(V5-V8) 27F/519R (V1-V3) 341F/806R (V3-V4) My concern is to have more...

25 August 2015 2,031 8 View

How to use labelled precursors to prove the originality of produced VOCs by bacteria in culture media?

I just need to confirm that the identified VOCs are actually produced by bacteria in bacterial culture media. And the ideal method is performing labeled precursors.

20 November 2014 7,308 4 View

Do I need an accurate mass instrument for global (untargeted) metabolomics?

I am going to do VOCs analysis using Shimadzu GCMS (it is not an accurate mass instrument). I just want to know if I will have problems with compound identification later by MSMS analysis.

06 November 2014 2,612 3 View

What is the best DNA extraction method from mix bacterial culture in broth media?

I have 10 ml LB inoculated by mix bacteria (G+ and G-). It may include several different phyla, genera and species. I am going to extract their DNA. I am looking for any good protocol or kit.

10 July 2014 7,928 2 View

How can I measure LOD, LOQ and reproducibility for non targeted VOCs analysis?

I am using GC MS, HS-SPME. I need to measure LOD, LOQ and reproducibility for my method.

04 June 2014 3,892 2 View

What are Y, M, W and D in primer design?

These are universal primers for 16S rRNA amplification; F24 (5’- GAG TTT GAT YMT GGC TCA G -3’) Y36 (5’-GAA GGA GGT GWT CCA DCC-3') What are the representative pairs for YMWD?

02 June 2014 140 16 View

Is it possible to use Retention index to confirm compound identification in non-targeted metabolomics?

I am going to use Retention index for compound identification. I will use NIST that provide me Retention index for hits. Method of extraction is SPME 1. I am not sure if I can use retention...

28 May 2014 5,280 2 View

How can an internal standard such as toluene-d8 be used for fecal VOCs quantification?

I am going to run GC-MS for headspace fecal sample's VOCs analysis. I will have about 300 putative compounds (non-targeted analysis) in each run. For compound quantification analysis, I need to...

13 May 2014 2,378 3 View

How can retention index be used for VOC identification?

I am going to use RI as a compound identification beside a NIST library search for VOCs. I am not sure if it can help me for non targeted VOC analysis where I have many peaks and potential...

22 April 2014 8,276 3 View

What is the best method of oral rinsing sample collection for harvesting only oral microbiota?

I will provide oral rinsing samples from patients using 10ml PBS followed by concentrating it into 1ml PBS. I need to separate oral microbiota in collected samples from epithelial cells, food...

22 April 2014 7,089 0 View

How can I do VOCs profiling based on traditional methods using GCMS?

I am going to do VOCs analysis based on the workflow below; MS acquisition- MS database search- Targeted MS/MS acquisition - Comparison MS/MS spectra- Comparative ID We have GC-triple Quad,...

20 April 2014 902 4 View

SingleQuad or TQuad? Can I use both of them for XCMS analysis?

I am going to analyze VOCs in bacterial culture media. My method of extraction is SPME and none-targeted.

16 April 2014 2,994 4 View

How can I use XCMS data in AMDIS for feature identification?

I have two GC/MS data-sets (positive and negative). About 2234 features have been detected by XCMS and 400 of them showed significant differences between those two groups. Now, I need to...

15 April 2014 3,356 1 View

How can I do global bacterial VOCs analysis by GC-MSMS?

I am going to analyse bacterial culture media for VOCs profiling. SPME is a used method for headspace VOCs extraction. Can I do VOCs profiling by using only one sample and one run GC-MSMS? Or I...

06 April 2014 1,119 2 View

Can I do GC/MSMS for volatile organic compounds (VOCs) profiling?

I am going to profile some human samples for profiling the VOCs. I want to use XCMS for processing and for the comparison of my outcome data and find the differences between my samples. For...

02 April 2014 1,533 5 View

Can I use XCMS for compounds identification?

I am going to run GC MS for VOCs profiling. But I do not know whether XCMS can identify the features or not.

19 March 2014 7,477 2 View

What are the differences between peptone, tryptone, tryptone peptone, trypticase, and trypticase peptone?

Reference to "Caldwell, D.R. and M.P. Bryant, Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Applied microbiology, 1966. 14(5): p. 794-801" I need to use...

18 March 2014 7,811 11 View

What is the difference between XCMS and MetaXCMS? Can I use them for GCMS data?

I am going to profile the VOCs of bacteria by GCMS. I just want to know if I can use these software for metabolites profiling.

03 February 2014 5,651 1 View

What is the best way to store fecal samples? How can I prepare the natural condition for fecal storage?

I am going to store fecal samples for culture dependent and culture independent bacterial diversity analysis.

27 November 2013 1,931 3 View

How can I find the similarities between GC chromatograms?

I have about 40 GC/MS chromatograms and want to find the similar peaks.

26 October 2013 3,050 3 View

How I can find the similarities of several GC/MS chromatograms? Can I relay of retention time or the best one is retention index?

I cultured a bacterium in 8 different culture conditions to find the VOCs cohort of this bacterium in different conditions. I am wondering if you can tell me the best way of data analysis by using...

22 October 2013 9,148 3 View

What percentage of sheep blood is the best for making BHI broth medium for fecal bacterial culture?

I want to make BHI broth and add blood to it. Is it okay if I add blood to the broth media without filtration or I need to filter it?

04 October 2013 383 1 View