Posts in ABRF Discussion Forum

Hi,

A few manufactures of polar or glycolipids recommend using glass pipet tips but
are they  absolutely necessary for handing solvent for glycolipids and solution
of glycolipids ?

Thanks.

Hi Chris. You could consider an S-trap cleanup/digestion
(www.protify.com/s-trap is a commercial source) approach following protein
extraction. Works well to remove polymers in our experience.
Erik

-----Original Message-----
From: ABRF Discussion Forum <email obscured>] On Behalf Of turck
Sent: Wednesday, January 15, 2020 9:49 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] exosome proteomics

We are interested in the exosome proteome and want to try the Thermo Exosome
Kits 4484453 and 4478359.

Following exosome isolation we will lyse and extract proteins and plan to
prepare them for mass spectrometry analysis with the FASP protocol.

The Thermo Exosome Kit employs polymers for isolating the exosomes and we are
concerned that they will later show up during mass spectrometry which may
affect data in a negative way.

Questions:
-	what kind of polymers are used in the Total Exosome Isolation Kit?
-	what size do the polymers have?
-	would you recommend the FASP protocol or some other method for protein
preparation with the goal to remove possible polymer contaminants?

Any advice would be greatly appreciated! We have previously used
ultracentrifugation methods for exosome isolation, but are not satisfied with
the yields.

Chris
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I agree.  Thermo should escalate this up to higher level people if engineer
cannot resolve the issue in a timely fashion.  The QE-Plus instruments are very
good and this is not acceptable.  Push Thermo to escalate to bring in more
experienced people promptly.

Randy


Randy Wilhelm
Analytical Chemist Fellow
Mallinckrodt Pharmaceuticals
(314)654-3965

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of Margaret Coe
Sent: Monday, January 6, 2020 3:28 PM
To: <email obscured>' <email obscured>>
Subject: [EXTERNAL] Re: [ABRF Discussion Forum] New Q Exactive Plus is down
after over a year in operation

CAUTION: This email originated from
<email obscured> which is outside of the
Mallinckrodt system. Do not click on any links or attachments unless you know
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have any doubts, please contact <email obscured> for assistance.

Hi Benjamin,
I would be e-mailing every day, after what you think is a reasonable period of
time.  2 months is ridiculously long!  Thermo does respond, but I have found
that much depends on the individual engineer.  Ask for their manager's name and
e-mail them, if you don't get some action soon.


Best regards,
Margaret Coe
Technologist
Equity Committee Chair

DDI +64 9 923 3432 Ext 83432 E <email obscured> W liggins.auckland.ac.nz A
The University of Auckland, Building 503, Level 2, 85 Park Road, Auckland P
Private Bag 92019, Auckland 1142, NZ




-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of benjamin
Sent: Monday, 6 January 2020 6:31 PM
To: <email obscured>
Subject: [ABRF Discussion Forum] New Q Exactive Plus is down after over a year
in operation

Hi

Happy New Year.

We have a Thermo QE+ in the lab and the system is barely over a year before the
turbopump broke down. Since the pump was replaced, the system has been
experiencing problems and has not been in operation for the past two months.
The local technician is still trying to find the mysterious cause while our
samples are piling up.

I know we could just wait out for the problem to be fixed but is it a good
idea? Does anyone have a similar encounter or able to advise as to how long we
should wait before discussing with Thermo for a more significant solution?

Alternatively, we could send the samples to Thermo regional lab but the number
of samples that can be run is limited and its at the customer's expense.

Benjamin
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Hi all,

We are looking for a LC-MS analyst to join our core Metabolomics facility at
the Cancer Research Beatson Institute in Glasgow UK.

The full Job posting can be found on the institutes careers site:

http://www.beatson.gla.ac.uk/Careers/Scientific-Officers/

This is a rare opportunity to join a funded core facility. Please share.

Many thanks,

David Sumpton

Despite unplugging our data system from the lan to prevent a forced win10
upgrade, the system went ahead and upgraded itself. I presume it had already
downloaded all the files. Initially everything worked, but midway through the
first day of operation, we lost ability to connect to the mass spec. We can
ping it successfully (so the network settings are correct), but when we select
it in the instrument configuration, the dialog closes, the windows circly thing
spins, and NOTHING. When we re-open the configuration utility, the mass spec is
unclicked. Note also that the LC (a 1290 stack) is connected through the same
switch and seems to work fine. All lc components appear and are controllable in
mass hunter. We are running masshunter 7.0. I don't think it was expressly
written to operate under windows 10. I am expecting that it can do so and that
our problem is solvable, but maybe not. We at first thought it was a firewall
issue because we were unable to shut the firewall off for the instrument
network (ITS manages these settings here). But, it has persisted even after
they shut off the firewall.

Any suggestions?

Thanks.

Noah


Assistant Professor
Sandra and Edward Meyer Cancer Center
Department of Biochemistry
Weill Cornell Medical College
413 East 69th Street, BRB1612
Telephone: 646-962-6232
E-mail: <email obscured>

Anoja,

Our facility used Tufts University Core Facility
(http://tucf-genomics.tufts.edu/) for several HiSeq 2500 runs when we
decommissioned our own instrument.  They were very responsive with good
turnaround times.

Best,

Nathan

-------------------------------------------------------------------------
Nathan J. Bivens
Director, DNA Core Facility
University of Missouri
216 Bond Life Sciences Center
Columbia, MO   65211

Phone   (573) 882-0428
Web  DNACore.missouri.edu

Follow the DNA Core on Twitter @MUDNACore

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of Perera, Anoja
Sent: Wednesday, January 08, 2020 1:13 PM
To: <email obscured>' <email obscured>>
Subject: [ABRF Discussion Forum] HiSeq 2500 Outsourcing

Hello,

I need to outsource 3 Rapid Runs for HiSeq 2500. If you are still running this
instrument type, and you can provide a reasonable turnaround time, can you
please contact me?

Thanks,

Anoja

Anoja Perera
Director, Sequencing and Discovery Genomics Stowers Institute for Medical
Research
1000 E 50th Street
Kansas City, MO 64110
816-926-4461


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Hey Kym

Sorry it was a lame answer. I would grab the IDEX catalog (obviously there are
other fittings suppliers) at

https://www.idex-hs.com/literature-tools/literature-downloads/catalogs/

download it, unzip it, and you have a nice resource locally. Alternatively if
you are like me, I typically like a hard copy in the lab as it can be easier to
browse for me. They send them upon request. You could call them too. They have
good operators often.

All the page numbers referred to here below will reference those.

First, I think it is an M6 and not M5. M6 is more common. I misspoke
previously. The “M” series is a metric thread rather than English. I think that
since it is a Shimadzu, it’s metric. Right? There are kinda two possibilities,
english or metric threads. Most all metric. It might be 1/4x28 if english, but
NO not likely. Pg31

Second, since there is no tubing in the pic I saw, I am assuming that you might
have to select tubing or else use tubing from something else existing. This is
can be fraught as the material compatibility of the tubing can matter. One can
leach things if a ‘bad’ polymer is selected for the tubing. So one would want
chemical compatibility, there are a few choices. I would cheat and just use
what any HPLC vender uses, I’d guess the high purity PFA might be a good choice
(pg15). These are all on pgs 24-27 in the catalog. You could just unscrew a
line from another hplc too. I assume the degasser will go in an existing HPLC

The tubing matters as the OD is important for selecting the fitting. For
solvent lines on the low pressure (pre-pump) side of things where the degasser
is one wants wider fatter tubing. Here one can choose metric OR english. Often
I find a 1/8th tubing with a metric thread fitting.

Now we have the fitting thread, M6 most likely, and the OD, for sake of
argument I will say 1/8th inch. The ports on these types of lines are flat
bottomed. They came from the days of flanged fittings I guess but no to many
use flanged as making a flanged fitting end is a drag. Hard to change the
fitting on them too. This is a ‘flat bottomed’ fitting. It has simple topology
compared to the the high pressure HPLC fittings. See this cool link for all the
port drawings
https://www.idex-hs.com/literature-tools/tools-drawings/standard-port-drawings/
and especially the M6 at
https://www.idex-hs.com/wp-content/uploads/2018/05/M6-standard-port-connection.pdf
its flat. For grins the “periodic table of the analytical fittings” is worth a
look at
https://www.idex-hs.com/wp-content/uploads/2018/05/Periodic-Table-of-the-Analytical-Fittings.pdf.zip

I like the p45 Flangeless fittings as they have longer thread lengths (std 0.48
“)to fill the female port before the knurled nut hits the degasser (the metric
M6 has 0.39”) but i am guessing that is not important and you don’t have a
longer choice.

So people use a fitting like the VacuTight pg 42, for that I’d say the P-945x
with P-940x Ferrule for 1/8th inch tubing. These ferrules also work with
P-307x, P-307Sx, P-347x, P945x (says pg42-43)

all this should get you close.

Matt from phone

Matt from phone

> On Jan 7, 2020, at 1:32 PM, Kym Faull <email obscured>> wrote:
>
> ― 2 file links ―
>
> Dear ABRF colleagues:  Attached  are pics of the Shimadzu DGU-14A degasser
that we have recently been given.  We need to connect to the solvent inlet and
outlet ports, but we do not have the correct fittings.  Does anyone recognize
this unit, and if so can you provide information about the type of fittings it
accepts for the solvent inlet and outlet lines?

>>
>> Thanks for taking the time to help with this.
>>
>> Kym
>> '
>> Kym Francis Faull, Ph.D.
>> Director, Pasarow Mass Spectrometry Laboratory
>> Jane and Terry Semel Institute for Neuroscience and Human Behavior at UCLA
>> Professor Emeritus, Department of Psychiatry and Biobehavioral Sciences
>> David Geffen School of Medicine at UCLA
>> Telephone: (310) 206 7881 (office)
>> Telephone: (310) 206 7886 (laboratory)
>> Facsimile: (310) 206 2161
>> Electronic mail: <email obscured> <email obscured>>
>>>
>>>
>>
>
>
> ― 2 files ―
>
>  □ IMG-0252.jpg  (2mb)
>      http://list.abrf.org/r/file/oKfzGjVlo0sGdBwnxZAMaxAygbM-7MyR-2MiaiR8/
>
>  □ IMG-0251.jpg  (2mb)
>      http://list.abrf.org/r/file/4pjUMaIfIEk8dZBfjZ0d5uCfDUw-8lM6-2MiaiRm/
>
> ――
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>

Dear ABRF colleagues:  Attached  are pics of the Shimadzu DGU-14A degasser that
we have recently been given.  We need to connect to the solvent inlet and
outlet ports, but we do not have the correct fittings.  Does anyone recognize
this unit, and if so can you provide information about the type of fittings it
accepts for the solvent inlet and outlet lines?

>
> Thanks for taking the time to help with this.
>
> Kym
> '
> Kym Francis Faull, Ph.D.
> Director, Pasarow Mass Spectrometry Laboratory
> Jane and Terry Semel Institute for Neuroscience and Human Behavior at UCLA
> Professor Emeritus, Department of Psychiatry and Biobehavioral Sciences
> David Geffen School of Medicine at UCLA
> Telephone: (310) 206 7881 (office)
> Telephone: (310) 206 7886 (laboratory)
> Facsimile: (310) 206 2161
> Electronic mail: <email obscured> <email obscured>>
>>
>>
>

IMG-0252.jpg 1811.5kb

IMG-0251.jpg 1943.7kb

What are the issues exactly? We've experienced 4-5 turbo replacement on two
QE-plus instruments in our lab and it's usually a straight forward service.

Bin


On Mon, Jan 6, 2020 at 12:30 AM benjamin <

<email obscured>> wrote:

> Hi
>
> Happy New Year.
>
> We have a Thermo QE+ in the lab and the system is barely over a year
> before the turbopump broke down. Since the pump was replaced, the system
> has been experiencing problems and has not been in operation for the past
> two months. The local technician is still trying to find the mysterious
> cause while our samples are piling up.
>
> I know we could just wait out for the problem to be fixed but is it a good
> idea? Does anyone have a similar encounter or able to advise as to how long
> we should wait before discussing with Thermo for a more significant
> solution?
>
> Alternatively, we could send the samples to Thermo regional lab but the
> number of samples that can be run is limited and its at the customer's
> expense.
>
> Benjamin
> ――
> View topic http://list.abrf.org/r/topic/UNzjx1uzQcMKNPpfCQprQ
> Leave group <email obscured>?Subject=Unsubscribe
>
>

A full-time research technician position is available in an independent
proteomics research group at Weill Cornell Medical College. The primary duties
of this position are to support the daily workings of the laboratory. However,
the ideal candidate will also be an active participant in laboratory research
and will have the opportunity to pursue independent projects.

Duties
-light administrative including ordering and maintaining a chemical inventory
-preparing stock solutions, stocking laboratory
-maintaining an orderly laboratory work environment
-experimental planning and design
-protein/peptide sample preparation
-data acquisition, analysis, and report generation

Requirements
*Bachelor’s or Master’s degree in chemistry, biochemistry, cell biology,
bioinformatics, or related field
*A strong interest in molecular biological science
*At least 1 year (or 2 summers) of related laboratory experience
*Strong organizational, planning, and record-keeping skills
*Strong computer skills - knowledge of excel, mathematica, matlab, R or basic
coding experience is desirable
*Excellent written and verbal communication skills.
*Attention to detail and good interpersonal skills.
*Preference given to those with previous HPLC or Mass Spectrometry experience

A two-year commitment is preferred.

For consideration, please submit resume/cv and cover letter along with the
names of three references to: Noah Dephoure - <email obscured>