Samantha Jeschonek

11 Questions 40 Answers 0 Followers

Questions related from Samantha Jeschonek

Tips for protein resolution: 65 vs 75 kD?

Due to limited sample, I'm trying to maximize each SDS gel/Western Blot that I run. In an ideal world, I'd like to resolve a 40 kD, 65 kD, and 75 kD protein on the same gel. I prefer to cut my...

20 November 2017 2,321 4 View

Does anyone know of a good resource for mass spec analysis workflow?

Hello all -- Does anyone have a good paper/book/website that goes through the analysis of (label-free) mass spec data starting from .raw files? I'm specifically looking for resources that use...

18 August 2017 7,426 8 View

Is it necessary to reverse formaldehyde xlink for Mass Spec analysis?

I am crosslinking cells with 0.1% formaldehyde and performing an IP in order to isolate protein-protein complexes. The downstream analysis for this experiment is mass spectrometry. I am...

07 August 2017 2,292 5 View

PhiX spike in necessary for RNA-seq?

We are sequencing through genewiz and see that they offer PhiX spike in controls. For normal RNA-seq (without major concern of limited sequence diversity), are Phix spike-in's necessary?

27 July 2017 8,023 2 View

My protein was detectable by Western Blot but not mass spec...ideas?

We did an IP experiment and sent the results for mass spec. I confirmed by western blot (on the same sample) that some positive controls were present -- including the antigen. The mass spec...

31 May 2017 5,762 4 View

Does anyone have a protocol for coating microscope slides with lipids?

Hi all -- We are hoping to coat microscope slides in the lipid DOPC. Does anyone have protocol for this?

18 May 2017 8,166 1 View

Sonication to help resuspend protein after acetone precipitation?

I'm preparing some samples for mass spectrometry. In order to remove interfering compounds (SDS, Tween20), I need to acetone precipitate my sample. I've had some difficulty getting my sample back...

05 May 2017 1,660 5 View

Avoid IgG contamination in mass spec WITHOUT antibody-crosslinking?

I'm new to mass spec/proteomics and hoping for some advice! We want to do mass-spec on the pulldown from an immunoprecipitation. We are concerned about IgG/antibody contamination in the...

02 April 2017 9,525 4 View

RIP Seq: Does it matter if negative control pulls down less total RNA than samples?

I am optimizing conditions for an RNA-IP Sequencing (RIP-seq) experiment. The goal is to identify associated RNAs that co-IP with a particular transcript.IPs will be performed with antibodies...

31 October 2016 1,530 5 View

RT-qPCR: Very different amplification curves between samples. Short linear phase? Drooping plateau?

I'm having some trouble with my RT-qPCR. Some of my amplification curves (delta RN vs cycle #) look as expected, but others have a distorted curve. High starting background that drops, followed...

05 October 2016 5,689 6 View

Does anyone have experience with RNA-IP: enrichment over input qPCR validation?

Hello - I have a question regarding the best way to setup a (two step) RT-qPCR experiment. I have performed an RNA-IP and using qPCR want to determine if a specific RNA is enriched over (1) input...

21 August 2014 897 9 View