Posts in ABRF Discussion Forum

Hi,

I am not aware of any alternative sources for the Capillary Arrays.  The lasers
can still be replaced through 3rd party Service Companies such as SeqGen
because ThermoFisher's legal hold on the lasers is only for the entire laser
box assembly... and the actual lasers are still being manufactured and sold to
companies other than ThermoFisher.  Thus, SeqGen can replace the laser
itself... and even has a compatible box should the original TF box electrical
connections be in bad shape.

However, given that no other machine uses the 3130's and 3130xl's capillary
arrays, I expect that ThermoFisher likely retained an absolute hold on whether
the arrays can be manufactured and sold... and it seems unlikely that any other
company would attempt to provide a knock-off version.  This is, I believe, the
method that ThermoFisher finally resorted to in order to force the 3130 series
into full retirement.

Personally, I think this overall strategy is a grand mistake on ThermoFisher's
part, but that's the course TF has chosen.  Equally unfortunately, the Applied
Biosystems SeqStudio Flex Genetic Analyzer (i.e., the latest replacement being
offered by TF for the 3130 series) maintains most of the failings of the 3500
series... making it equally unsuitable as a replacement for moderate throughput
facilities which need to minimize costs in order to remain viable.

Sincerely,

Scott Herke
Manager, Genomics Facility
Louisiana State University
<email obscured>

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of mmartinez
Sent: Monday, April 18, 2022 9:49 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] ABI3130/xl Reagents discontinued

Hello,

You have probably already heard that Thermofisher will discontinue the
provision of reagents and parts (like capillary array) for sequencers
ABI3130/xl.

Do you know if there are other brands to buy similar products?

Thank you!


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Dear ABRF's SENPAI:

Has anybody had good experiences with the mass spectrometry detection of
sulfonated cysteine peptides (Cys-SO3H with a monoisotopic mass addition of
47.9847 Da to Cys residue) vs perthiosulfenated cysteine peptides (Cys-SSOH
with a monoisotopic mass addition of 47.9670 Da tp Cys residue)? Can the
Cys-SSOH peptides survive with DTT reduction?  We are dealing with in-gel
tryptic digestion samples.  I understand that probably one can tell the
difference with a well calibrated and high resolution mass spectrometer.  Are
there any signature peaks or neutral loss for either of them?

Thank you in advance.


Geeng-Fu


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Dear Steve,

according to the experience of several of our customers, relocation of an ABI
3730(xl) is possible WITHOUT the need to perform laser alignment and new
spectral calibrations, afterwards. Please do the following:
1. perform 2x spatial with fill -> record a screenshot of the second spatial
2. secure the reagents and autosampler arm for transport: replace anode and
cathode buffer by purified water (in case something spills over during
transport), seal the anode buffer level hole with sticky tape and secure the
vial by placing some matching piece of foam material below it, with instrument
turned off remove water and water plates and use a rope or sticky tape to lock
the autosampler arm to the frame of the autosampler station (so that the arm
will not change it's position / fall down during transport, capillary array
will stay installed with electrode ends in the water filled buffer vial)
3. uninstall PC, monitor and accessories and label / remember the socket
position for the network cable between PC and ABI 3730xl (because of the fixed
IP address)
4. handle the sequencer gently during transport: remove the 4 feeds and put
2-3" thick foam material below the complete bottom of the sequencer (to avoid
heavy transport shocks onto the laser and optical system), also secure the
sequencer's outside by wrapping with bubble foil, during transportation secure
the sequencer on the 2-3" foam material against moving or flipping over
5. at the new location: reassemble instrument and PC and accessories, remove
the autsampler blocking rope / tape, replace water with buffer, open the buffer
level hole
6. perform 2x spatial with fill -> record a screenshot of the second spatial
and compare with the screenshot from before the movement -> if not more than
10% less signal compred to before movement, there is no need to perform laser
alignment and / or new spectral calibrations -> if more than 10% minimum
perform new spectral calibrations. Optical sensitivity / spatial peak heights
usually decrease 15-25% each year by general ageing / laser-missalignment
effects.


Good luck,
AXEL

-----Ursprüngliche Nachricht-----
Von: ABRF Discussion Forum <email obscured>] Im Auftrag von Keefe,
Robert G (HEALTH)
Gesendet: Mittwoch, 9. März 2022 17:24
An: <email obscured>
Betreff: Re: [ABRF Discussion Forum] DNAseq: how to move a 3730

It's been a while since I needed to pay attention to such details, but I
believe you may also need to perform some kind of preventative maintenance
procedure to stabilize the laser unit before it is crated & transported to its
new home.

Bob Keefe
Wadsworth Center, NYS DOH

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of hartson.steve
Sent: Wednesday, March 9, 2022 11:10 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] DNAseq: how to move a 3730

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Hello all,

We are planning to move a 3730 DNA sequencer appr. 100 miles.  I'm wondering
what's entailed WRT prepping it for the move, and whether or not I need
engineer support to do so.  Comments?

Cheers!

Steve
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Esteban, please see sample email

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Hi Esteban,

The verification codes I get are texted from 631-898-5820

Best,
Allis

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> On Mar 27, 2022, at 1:32 PM, Winn, Mary <email obscured>> wrote:
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> Esteban,
>
> I was able to access the Attendee HUB through the meeting website -
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> From: ABRF Discussion Forum <email obscured>> on behalf of ABRF - Frances
Weis-Garcia <email obscured>>
> Date: Sunday, March 27, 2022 at 4:24 PM
> To: <email obscured> <email obscured>>
> Subject: [External] Re: [ABRF Discussion Forum] ABRF meeting verification
email
> Esteban,
>
> I do not know, but have forwarded your inquiry to someone in our association
management team who should be able to help you. If you do not get a response by
3 pm PT please “text” me through the meeting app and my email. I will check
them both a little after 3 pm.
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> If you have any other questions at the meeting, please reach out through the
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> Frances Weis-Garcia
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> Sent on the fly from my mobile device
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> On Mar 27, 2022, at 12:03 PM, G. Esteban Fernandez
<email obscured>> wrote:
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> Hi everyone,
>
> Would someone who is attending the meeting virtually please tell us the
e-mail address that the app/website verification e-mail came from? I need to
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> Thanks!
>
> G. Esteban Fernandez, PhD | Imaging Scientist
> Cellular Imaging Core | The Saban Research Institute
> Children's Hospital Los Angeles
> 4650 Sunset Blvd.<x-apple-data-detectors://1>, Mailstop #135  |  Los Angeles,
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Esteban,

I do not know, but have forwarded your inquiry to someone in our association
management team who should be able to help you. If you do not get a response by
3 pm PT please “text” me through the meeting app and my email. I will check
them both a little after 3 pm.

If you have any other questions at the meeting, please reach out through the
app.  If you are new to ABRF or just want to learn more about the association,
please be sure to attend the new members meeting at 4 pm today.

Looking forward to seeing you at the meeting!

Be well

Frances Weis-Garcia

Sent on the fly from my mobile device

On Mar 27, 2022, at 12:03 PM, G. Esteban Fernandez
<email obscured>> wrote:

Hi everyone,

Would someone who is attending the meeting virtually please tell us the e-mail
address that the app/website verification e-mail came from? I need to exempt it
from my spam filter.

Thanks!

G. Esteban Fernandez, PhD | Imaging Scientist
Cellular Imaging Core | The Saban Research Institute
Children's Hospital Los Angeles
4650 Sunset Blvd.<x-apple-data-detectors://1>, Mailstop #135  |  Los Angeles,
CA 90027<x-apple-data-detectors://2/0>
Ph: 323.361.2548<tel:323.361.2548> | Fax: 323.361.1549<tel:323.361.1549>
<email obscured><email obscured>>
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I have a few concerns here.

There has been zero public discussion about this project, and when I
pressed the organizer Kris Kublow about issues with the forward model and
PSF used in the simulation of nuclei images, he was polite, but answered
none of my concerns.   He did promise that the issues would be cleared up
"soon".   I had expected they would be cleared up before the workshop, so
all groups would be on equal footing.

My main concern is with the forward model used to generate the Nuclei
images.  The original PSF used in the project was highly under-sampled
and had to be resampled inside the simulation.   The Nuclei images require
deconvolution to get the best answer however the deconvolution required a
'trick' because of the sampling issue.

So my concern is the results will depend on the company, or group behind
the software 'knowing' tricks.  Who are the experts that are going to be
involved in the workshop?  Do they have the required math background
(signal process, DSP, image processing math) or are they more on the
marketing or support side?  What companies and open source groups are
involved?  Would they be willing to present their solutions before hand so
other experts can evaluate?

Brian

ABRF

On Fri, Mar 18, 2022 at 7:30 AM GroupServer Administrator <email obscured>>
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Yea! I know how it feels when something goes amiss.

All the best,


Eric

D. Eric Anderson,    Ph.D
Advanced Mass Spectrometry Core Facility, NIDDK
NIH


Building 8 Room B2A19, 9000 Rockville Pike, Bethesda MD, 20892 USA
(301)-496-7546

________________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of Chen, Zhuo, Dr.
<email obscured>>
Sent: 09 March 2022 12:07
To: <email obscured>
Subject: [EXTERNAL] Re: [ABRF Discussion Forum] SDC precipitation issue

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Dear Eric,
Great tip! Indeed, my TECP solution was apparently acidic and after adjusting
the pH, it is all clear now. Thank you so much!

Zhuo

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of Anderson, David
Eric (NIH/NIDDK) [E]
Sent: 09 March 2022 17:59
To: <email obscured>
Subject: Re: [ABRF Discussion Forum] SDC precipitation issue

My guess is you are too acidic - check the pH of the TCEP solution and if it is
acidic that would be consistent. If that is the case  you can try slowly moving
the pH up by adding tiny amounts of base until it clears. It is also possible
it is specific to the TCEP addition (I have little experience with TCEP and
soaps but some things do specific aggregation).

Eric

D. Eric Anderson,    Ph.D
Advanced Mass Spectrometry Core Facility, NIDDK NIH


Building 8 Room B2A19, 9000 Rockville Pike, Bethesda MD, 20892 USA
(301)-496-7546



________________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of Chen, Zhuo, Dr.
<email obscured>>
Sent: 09 March 2022 11:53
To: <email obscured>
Subject: [EXTERNAL] [ABRF Discussion Forum] SDC precipitation issue

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Hello all,
I just start to try digestion with SDC, I resuspended my protein pellet
(Acetone precipitated) with 1% SDC in 50 mM HEPES buffer (pH 7.5) and when I
add TCEP to 10 mM, my solution turned total milky. I have not clue what is
going on. Should I use a different buffer instead of HEPES?

Thank you!

Zhuo Chen

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My guess is you are too acidic - check the pH of the TCEP solution and if it is
acidic that would be consistent. If that is the case  you can try slowly moving
the pH up by adding tiny amounts of base until it clears. It is also possible
it is specific to the TCEP addition (I have little experience with TCEP and
soaps but some things do specific aggregation).

Eric

D. Eric Anderson,    Ph.D
Advanced Mass Spectrometry Core Facility, NIDDK
NIH


Building 8 Room B2A19, 9000 Rockville Pike, Bethesda MD, 20892 USA
(301)-496-7546

________________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of Chen, Zhuo, Dr.
<email obscured>>
Sent: 09 March 2022 11:53
To: <email obscured>
Subject: [EXTERNAL] [ABRF Discussion Forum] SDC precipitation issue

CAUTION: This email originated from outside of the organization. Do not click
links or open attachments unless you recognize the sender and are confident the
content is safe.


Hello all,
I just start to try digestion with SDC, I resuspended my protein pellet
(Acetone precipitated) with 1% SDC in 50 mM HEPES buffer (pH 7.5) and when I
add TCEP to 10 mM, my solution turned total milky. I have not clue what is
going on. Should I use a different buffer instead of HEPES?

Thank you!

Zhuo Chen

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It's been a while since I needed to pay attention to such details, but I
believe you may also need to perform some kind of preventative maintenance
procedure to stabilize the laser unit before it is crated & transported to its
new home.

Bob Keefe
Wadsworth Center, NYS DOH

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of hartson.steve
Sent: Wednesday, March 9, 2022 11:10 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] DNAseq: how to move a 3730

ATTENTION: This email came from an external source. Do not open attachments or
click on links from unknown senders or unexpected emails.


Hello all,

We are planning to move a 3730 DNA sequencer appr. 100 miles.  I'm wondering
what's entailed WRT prepping it for the move, and whether or not I need
engineer support to do so.  Comments?

Cheers!

Steve
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