Posts in ABRF Discussion Forum

Hello ABRF community,

At my institution, the current managers of our Cesium Irradiator and X-Ray
Irradiator would like these facilities to run as a core, with administration
handled by our centrally run University Shared Resources program. I am the
director of this program. I have limited knowledge on how these facilities
should be run.

Is there anyone in ABRF that has experience with these who could give me
insights and start me down the right path for investigating this? I’d like to
know if it’s appropriate to run as a standard core, and if so, what might be
required to set this up optimally.

Thanks for any help you can offer!
Andy Chitty
OHSU

That's crazy!  What does illumina think is happening to the libraries at
different temperatures?  Simple degradation doesn't seem like it would explain
that



Charles Nicolet, Ph.D
Research Associate, Farnham Lab
Los Angeles, CA 90033
Lab: 323-442-7757
Direct: 530-304-1137

Rest of post

________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of Reardon, Claire
Bailey <email obscured>>
Sent: Thursday, May 23, 2019 8:30 AM
To: <email obscured>
Subject: Re: [ABRF Discussion Forum] NovaSeq index hopping

Hi Stuart,

Here's what we heard from Illumina about this issue:

1. Expected rate of mis-assigned indexes on a non-patterned flowcell: 0.02%
2. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at -20: <0.5%
3. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at 4 degrees: <0.8%
4. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at RT: <8%
5. Expected rate of mis-assigned indexes on a patterned flowcell for a PCR-free
library: <2%

Bottom-line is we use UDIs for our Kapa libraries but still feel comfortable
running PCR-amplified libraries without UDIs as long as they were properly
stored.

I hope this helps, happy to chat more off-line about our experience so far.
Claire

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of slevine
Sent: Thursday, May 23, 2019 10:00 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] NovaSeq index hopping

Hello ABRFers,

We've started sending a lot of samples for NovaSeq and the topic of unique dual
indexes (UDIs) come up. Has anyone done any nice studies looking at how much of
an issue this really is? The mantra since
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_125724v1&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=2Qyimf36TXKijRVBkrWSfA&m=Weyzysa8qjLDHP__9Yj32xGLckr9MA5abGJxOCRkZMM&s=yq3qGhnEBh3AwYmuqj-WK0bGFBZLSYOa_cfBC2yuNGA&e=
has been to use UDIs on all ExAmp instruments but Illumina has certainly been
working to lower the rate also. In talking with folks from SeqWell yesterday,
in their literature they say their internal rate is 1:10,000 with their product
that does not have UDIs based on an iSEQ. They compare that to 1:250 for a
'conventional' prep. 1:250 is high, but not awful for most applications
certainly, and makes me wonder if UDIs are strictly necessary for most research
applications (obviously going in informed). This leads to these questions:

1. How well does iSEQ mimic NovaSeq for index hopping?
2. If you do a good job cleaning out free oligo, how much of an issue is index
hopping on NovaSeq with routine applications (NextFlex, Kapa, SMARTseq, etc.)

-Stuart

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Hi Stuart,

Here's what we heard from Illumina about this issue:

1. Expected rate of mis-assigned indexes on a non-patterned flowcell: 0.02%
2. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at -20: <0.5%
3. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at 4 degrees: <0.8%
4. Expected rate of mis-assigned indexes on a patterned flowcell for a
PCR-amplified library stored at RT: <8%
5. Expected rate of mis-assigned indexes on a patterned flowcell for a PCR-free
library: <2%

Bottom-line is we use UDIs for our Kapa libraries but still feel comfortable
running PCR-amplified libraries without UDIs as long as they were properly
stored.

I hope this helps, happy to chat more off-line about our experience so far.
Claire

Rest of post

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of slevine
Sent: Thursday, May 23, 2019 10:00 AM
To: <email obscured>
Subject: [ABRF Discussion Forum] NovaSeq index hopping

Hello ABRFers,

We've started sending a lot of samples for NovaSeq and the topic of unique dual
indexes (UDIs) come up. Has anyone done any nice studies looking at how much of
an issue this really is? The mantra since
https://www.biorxiv.org/content/10.1101/125724v1 has been to use UDIs on all
ExAmp instruments but Illumina has certainly been working to lower the rate
also. In talking with folks from SeqWell yesterday, in their literature they
say their internal rate is 1:10,000 with their product that does not have UDIs
based on an iSEQ. They compare that to 1:250 for a 'conventional' prep. 1:250
is high, but not awful for most applications certainly, and makes me wonder if
UDIs are strictly necessary for most research applications (obviously going in
informed). This leads to these questions:

1. How well does iSEQ mimic NovaSeq for index hopping?
2. If you do a good job cleaning out free oligo, how much of an issue is index
hopping on NovaSeq with routine applications (NextFlex, Kapa, SMARTseq, etc.)

-Stuart

――
View topic http://list.abrf.org/r/topic/6p7C8hMsdbCKuKhhhDINHK
Leave group <email obscured>?Subject=Unsubscribe

Hello ABRFers,

We've started sending a lot of samples for NovaSeq and the topic of unique dual
indexes (UDIs) come up. Has anyone done any nice studies looking at how much of
an issue this really is? The mantra since
https://www.biorxiv.org/content/10.1101/125724v1 has been to use UDIs on all
ExAmp instruments but Illumina has certainly been working to lower the rate
also. In talking with folks from SeqWell yesterday, in their literature they
say their internal rate is 1:10,000 with their product that does not have UDIs
based on an iSEQ. They compare that to 1:250 for a 'conventional' prep. 1:250
is high, but not awful for most applications certainly, and makes me wonder if
UDIs are strictly necessary for most research applications (obviously going in
informed). This leads to these questions:

1. How well does iSEQ mimic NovaSeq for index hopping?
2. If you do a good job cleaning out free oligo, how much of an issue is index
hopping on NovaSeq with routine applications (NextFlex, Kapa, SMARTseq, etc.)

Rest of post

-Stuart

In addition to software installation, you also need to perform autosampler
calibration, wavelength correction. You need standard array to do wavelength.

Hi all,

We have just one ABI 3130xl with a corrupt harddrive, and we don't have the
data collection software.

Does anyone have it somewhere where we could download it to get moving again?

Our lab has stopped now for days, and Thermofisher said we need the CD to do a
reinstall, but we can't find it (seems we never got it with the 2nd hand 3130
we bought).

Especially if someone in Melbourne Australia has the CD we could borrow to make
a copy??????

Vernon Muir
DNA SOLUTIONS
03 9800 1550

Hi all,

We have just one ABI 3130xl with a corrupt harddrive, and we don't have the
data collection software.

Does anyone have it somewhere where we could download it to get moving again?

Our lab has stopped now for days, and Thermofisher said we need the CD to do a
reinstall, but we can't find it (seems we never got it with the 2nd hand 3130
we bought).

Especially if someone in Melbourne Australia has the CD we could borrow to make
a copy??????

Vernon Muir
DNA SOLUTIONS
03 9800 1550

fyi - open mass spec scientist position in Newark, CA.  Contact Mary Heeney
<email obscured>, 650-521-2884) if interested.


www.intabio.com<http://www.intabio.com>


Best,

Allis



Lab move news: https://mass-spec.stanford.edu/sums-move-bbb

Rest of post

____________________________________________________________

Allis Chien, Ph.D.
Director, Stanford University Mass Spectrometry


Vincent Coates Foundation Mass Spectrometry Laboratory
Stanford Cancer Institute Proteomics Shared Resource
333 Campus Drive
Seely G. Mudd Building, room 167A, MC 5080
Stanford, CA 94305-4401

Ph: 650.723.0710<tel:650.723.0710>
Em: <email obscured><email obscured>>
http://mass-spec.stanford.edu
____________________________________________________________

BPI West 2019 Poster-FINAL.pdf 1431.6kb

Intabio_IntroHire_Apr2019.pdf 1584.9kb

Mass Spec Scientist Final.pdf 244.4kb

Hello all,

I would like to know what your favorite software platform is for doing quality
control of the sequence of cloned cDNA.  The purpose of course is primarily to
show that the cDNA you are using in your experiments is the correct sequence.
But also should collaborators/journals/funding agencies require the proof that
the clone is authentically what you say it is, you can provide them with a file
or set of files as evidence.

I've started looking around at software and see that DNA Baser sequence
assembly software appears to have a nice interface which has the
electropherogram above the text alignment in the same window.  This would allow
for efficient resolution of conflicts between different sequence runs.  You can
save the data for input later into the same program but I haven't seen how you
would save data to provide to another who may not have this software, or to
provide to a journal for e.g. supplementary data etc.

Thanks in advance for any input.

Rest of post

Brian

All inputs here are very helpful. Thank you so much for the suggestions.
Susie

On Sun, Apr 21, 2019, 10:16 AM Hampton, Brian <email obscured>>
wrote:

Rest of post

> Hello Susie,
>
> I've moved my lab several times, once between cities, twice between
> buildings on campus and numerous times between labs within a building.  In
> my experience, the instrument vendors don't actually move the instruments,
> maybe some do.  The service people I had basically did a quick checkout to
> verify working order, then shut it down, disconnect, and do the reverse
> when the instrument arrives at the new location.  I was responsible for the
> moving.  If something breaks during the move then its possible the mover's
> liability insurance will cover it.  That has never happened to me.  I've
> had movers transport triple quads, ion traps (not orbitrap) HPLCs Biacore
> etc.  No problem.  Once, we purchased an Agilent MALDI-TOF back in the late
> 1990s.  It was fairly small and on wheels.  It arrived on a truck wrapped
> simply in plastic.  The service engineer said they had less damage when the
> delivery people could see the instrument through the plastic wrap versus
> when it was crated and they could slam the crate around.
>
> Moving within a building with their smooth floors is easy if you have the
> muscle power, and good carts, or a lift cart that can be positioned at the
> bench height to slide heavy equipment off the bench to the cart at the same
> height.  I've done this by myself to move an LTQ.  That instrument isn't
> that big but wow is it heavy!  A student and I moved an LTQ Orbitrap
> "Classic" from one floor to another.  It rolls fairly easy.  The vacuum
> pumps are moved separately and that was harder than moving the Orbitrap.
> WRT the Orbitrap, the central electrode power supply is on the left side of
> the instrument toward the bottom.  It is held on with rubber isolation
> mounts, which as rubber is prone to do, degrade with time and so that power
> supply can drop down and then sit on the cables that connect through the
> bottom of the power supply.  This will happen just sitting still, but could
> be accelerated during moving.  So best to check these mounts, or try to add
> some support to help it hang in place during the move.  This should only be
> a problem on older instruments such as the Classic etc that have been in
> the field for some time.
>
> Moving between buildings, even if close, is best done via trucks because
> they will provide a much smoother ride compared to rolling carts etc. down
> the sidewalk.  Anything prone to vibrational damage should go on a truck no
> matter how small.
>
> If the path to the moving truck and back off at the new location is
> smooth, then I would just push the orbitrap onto and off of the truck into
> the new location.  However, the transitions from hallways to loading docks
> to trucks usually isn't smooth.  So its best to have it palatized to allow
> the movers to more "gently" traverse these transition points and use
> lifting equipment to facilitate loading and off loading. Once on the truck
> and secured, it will feel the same G-forces during the travel whether or
> not is palatized.  Possibly high frequency vibrations would be reduced if
> palatized vs not.  You could get a quote from Craters and Freighters if you
> don't want to have Thermo do it.
>
> Finally, it probably wasn't your decision to move.  So it would be logical
> to conclude that those who found it necessary to move should have a budget
> to pay for the move.  You need the instruments to work at the new
> location.  So at least in the case of the Orbitrap, if Thermo guarantees
> that it will work once moved - if they move it - then pay for them to do
> just that. If your institution balks a paying for that level of service,
> and it breaks in transit, then your institution should pay for repairs, if
> the mover's liability insurance doesn't.  For example, the central
> electrode power supply for the Orbitrap "classic" costs about $22,000.
>
> Cheers,
>
> Brian
> ________________________________
> From: ABRF Discussion Forum <email obscured>> on behalf of Bin Fang <
> <email obscured>>
> Sent: Saturday, April 20, 2019 7:39 PM
> To: ABRF Discussion List
> Subject: Re: [ABRF Discussion Forum] Mass spec moving service
>
> We did that 3 years ago. All bench top instruments should be easy to move.
> Just take tons of pictures before you disconnect the components. Then you
> can roll them on carts or benches with wheels. I'd be very scared to move
> the old LTQ-orbitrap. That instrument is probably the only one I would ask
> Thermo to move.
>
>
>
>
>
> On Sat, Apr 20, 2019 at 6:58 PM Mawuenyega, Kwasi <email obscured>>
> wrote:
>
> > Hi Susie,
> >
> > My lab recently moved to a different building and I was in a similar
> > situation. The solution I found (with a significant risk) was to hire a
> > moving company to help with transportation. Professional movers are
> insured
> > to cover damages up to a certain cost and they can tell you if your
> > expensive instruments can be covered under their insurance. If there is
> > anyone in your lab that knows how to take the instruments apart, that
> will
> > save you a bunch of money. If the pumps and accessories are taken off,
> the
> > MS itself can be rolled down the hall on carts or transported gently
> with a
> > truck. There's no need to open the MS itself and tilting during
> > transportation should be avoided at all cost. One Orbitrap Lumos, Fusion
> > and triple quads were move and reassembled at the new location without a
> > glitch. If you do not have anyone in-house to disassemble the
> instruments,
> > then you will have to go with the vendors to be safe.
> >
> > I hope this helps.
> >
> > Kwasi
> >
> >
> > -----Original Message-----
> > From: ABRF Discussion Forum <email obscured>> On Behalf Of Susie
> > Sent: Thursday, April 18, 2019 10:14 AM
> > To: ABRF Discussion List <email obscured>>
> > Subject: [ABRF Discussion Forum] Mass spec moving service
> >
> > Hi all:
> > We are moving our orbit trap, LTQ, and GCMS from one building to a new
> one.
> > The quotes we got from a vendor is very high. Any comments/thoughts/ideas
> > for how to move?
> > We moved the LTQ from one room to the other room by ourselves before. But
> > now with a new building and an orbitrap, we kind of hope to get a better
> > handle.
> > Appreciate your inputs on this!
> > Susie
> >
> > ――
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> >
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Hi Everyone,

I'm wondering if anyone can recommend any articles that document ionization
efficiency of peptides with and without adducts, or any empirical studies that
look at multiple parameters that affect ionization efficiency of peptides using
ESI?

Rest of post

Best,

Adam

We are seeking a Proteomics Core Manager (successor of Achim Treumann).

apply here: https://bit.ly/2vjVxOG

Salary:  £40,792 - £48,676

Closing date:  18 May 2019

Newcastle University Protein and Proteome Analysis (NUPPA) Core Facility is
looking to recruit a Senior Experimental Scientific Officer to oversee and
manage the high-end core technical facilities providing a state-of-the-art Mass
Spectrometry, Proteomics and Protein Production Facility for researchers
throughout the Faculty of Medical Sciences. You will provide the driving force
to develop and maintain a world leading capability in this key set of
technologies for the Faculty.

You will lead a successful and experienced team of four core technologists
offering Proteomics, Protein Production and Protein Biophysics services to all
researchers within the University and also commercial partners. The post is
required to manage, develop and promote these services within the University
and to national and international customers, both academic and industrial.

Possessing a relevant first degree or equivalent qualifications or experience,
and ideally with a higher degree, you will be an experienced Proteomics
professional with a biological background and experience in working within an
academic research environment and/or core technology facility. Your technical
skills should include extensive experience in LC-MS, MALDI-TOF, chromatographic
and electrophoretic techniques, and up-to-date data analyses workflows. You
should have experience of managerial responsibility for the scientific,
business and financial planning of a group and an understanding of cost
recovery regulations applied to a higher education setting.

Informal enquiries in the first instance should be made to Matthias Trost
<email obscured>)  or Rebecca Kenyon
<email obscured>)

http://www.ncl.ac.uk/NUPPA/

Newcastle University is committed to being a fully inclusive Global University
which actively recruits, supports and retains staff from all sectors of
society.  We value diversity as well as celebrate, support and thrive on the
contributions of all our employees and the community they represent.  We are
proud to be an equal opportunities employer and encourage applications from
everybody, regardless of race, sex, ethnicity, religion, nationality, sexual
orientation, age, disability, gender identity, marital status/civil
partnership, pregnancy and maternity, as well as being open to flexible working
practices.

click here for further details

Dear Manfred

At least two more.

AAA: Durrum D500
Protein sequencing: LKB solid phase sequencer

Regards,
Peter



On 20/04/2019 11:30, Manfred@newtoncon wrote:
> Hi,
>
> I am going to write a paper about the technical developments in Proteomics
and before, as protein analysis.
>
> Working in protein analysis for many years, as many of you, we went through
numerous technical and method developments – which disappeared quite fast and
never came back, like peptide ladder sequencing. And we spenttime to follow
such developments and found out, they do not help at all. Thinking back – I
feel like a Proteomics tomb rider ☺
>
> For this I am looking for information about:
>
> Protein sequencers (ABI, Beckman, Millipore, Knauer, Shimadzu and – if
available – more) and C-terminal sequencers
>
> Amino acid analysers (ABI, HP, Beckman, LKB and who else)
>
> Preparative gel electrophoresis (ABI, Biorad, LKB……)
>
> Developments as the ABI plotter, the converted autosampler to a fraction
collector), static nano spray, and what else comes into mind
>
> Analytical developments: MudPIT, in-source decay, peptide-ladder sequencing,
PVDF plotting and sequencing….
>
> I will also include mass spectrometers, like the first MALDIs, PDMS (I used
one), early TSQs (had an API III, API 100), HPLC/FPLC equipment (still see some
LKBs around), electrophoresis (still active but also some older developments),
>
> And what else comes in your mind, please throw it on me and please use
mypersonal email: <email obscured>
>
> I am also looking for contributors – as co-authors, talked to some people and
they like the idea, also to prevent the newbies to make the same errors we went
through

Rest of post

>
> Many thanks
>
> Manfred
>
>
>
>
> ――
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> Leave group <email obscured>?Subject=Unsubscribe
>

Hi Manfred,
Keith is right, listing just the keywords will generate as many characters as
what is required to write a paper...
Looking forward to dig into old transparencies, positive slides, hand-written
paper, needle printer, all this to remember the beginning of the proteomics
era...

A few keywords:
Definition of the word proteome in 1994 in Siena (M Wilkins)
Definition of the word proteomics in 1996 in Siena (M Wilkins / R Appel) and
published by P James in 1997
AA analysis and AACompIdent
PMF, AMT
LC-MALDI using a prototype lc spotter on a maldi plate
The Molecular scanner
The MALDI imaging development
ICAT, TMT, ITRAC, SILAC, ...
COFRADIC
AQUA, SISCAPA
Protein chips
2D-PAGE, 2D-DIGE
SELDI
And all the software and databases developed for this (see the Expasy.ch
old-tools page for a start) (ExPASy was the first website dedicated to life
sciences, and still exists since 1993)

Rest of post

Enjoy!

Pierre-Alain

-----Message d'origine-----
De : ABRF Discussion Forum <email obscured>> De la part de Ashman, Keith
Envoyé : dimanche 21 avril 2019 01:58
À : <email obscured>
Objet : Re: [ABRF Discussion Forum] History of Proteomics and before

Hi Manfred
Sounds more like a book. Solid phase sequencing, peptide synthesis. 2d gels and
in gel digest and the trypsin and other digest sin all their flavours come to
mind Gruß Keith


Sent from my iPhone

> On 21 Apr 2019, at 3:01 am, Manfred@newtoncon <email obscured>> wrote:
>
> Hi,
>
> I am going to write a paper about the technical developments in Proteomics
and before, as protein analysis.
>
> Working in protein analysis for many years, as many of you, we went
> through numerous technical and method developments – which disappeared
> quite fast and never came back, like peptide ladder sequencing. And we
> spent time to follow such developments and found out, they do not help
> at all. Thinking back – I feel like a Proteomics tomb rider ☺
>
> For this I am looking for information about:
>
> Protein sequencers (ABI, Beckman, Millipore, Knauer, Shimadzu and – if
> available – more) and C-terminal sequencers
>
> Amino acid analysers (ABI, HP, Beckman, LKB and who else)
>
> Preparative gel electrophoresis (ABI, Biorad, LKB……)
>
> Developments as the ABI plotter, the converted autosampler to a
> fraction collector), static nano spray, and what else comes into mind
>
> Analytical developments: MudPIT, in-source decay, peptide-ladder sequencing,
PVDF plotting and sequencing….
>
> I will also include mass spectrometers, like the first MALDIs, PDMS (I
> used one), early TSQs (had an API III, API 100), HPLC/FPLC equipment
> (still see some LKBs around), electrophoresis (still active but also
> some older developments),
>
> And what else comes in your mind, please throw it on me and please use
> my personal email: <email obscured>
>
> I am also looking for contributors – as co-authors, talked to some
> people and they like the idea, also to prevent the newbies to make the
> same errors we went through
>
> Many thanks
>
> Manfred
>
>
>
>
> ――
> View topic
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I agree with Keith, Manfred, this sounds more like a book
And it would be a valuable resource!
Deb McMillen

Rest of post


> Hi,
>
> I am going to write a paper about the technical developments in Proteomics
> and before, as protein analysis.
>
> Working in protein analysis for many years, as many of you, we went
> through numerous technical and method developments â which disappeared
> quite fast and never came back, like peptide ladder sequencing. And we
> spent time to follow such developments and found out, they do not help at
> all. Thinking back â I feel like a Proteomics tomb rider âº
>
> For this I am looking for information about:
>
> Protein sequencers (ABI, Beckman, Millipore, Knauer, Shimadzu and â if
> available â more) and C-terminal sequencers
>
> Amino acid analysers (ABI, HP, Beckman, LKB and who else)
>
> Preparative gel electrophoresis (ABI, Biorad, LKBâ¦â¦)
>
> Developments as the ABI plotter, the converted autosampler to a fraction
> collector), static nano spray, and what else comes into mind
>
> Analytical developments: MudPIT, in-source decay, peptide-ladder
> sequencing, PVDF plotting and sequencingâ¦.
>
> I will also include mass spectrometers, like the first MALDIs, PDMS (I
> used one), early TSQs (had an API III, API 100), HPLC/FPLC equipment
> (still see some LKBs around), electrophoresis (still active but also some
> older developments),
>
> And what else comes in your mind, please throw it on me and please use my
> personal email: <email obscured>
>
> I am also looking for contributors â as co-authors, talked to some
> people and they like the idea, also to prevent the newbies to make the
> same errors we went through
>
> Many thanks
>
> Manfred
>
>
>
>
> ââ
> View topic http://list.abrf.org/r/topic/5mQTpwQ3pNsTt8hr6V1GtA
> Leave group <email obscured>?Subject=Unsubscribe
>
>
>

Hello Susie,

I've moved my lab several times, once between cities, twice between buildings
on campus and numerous times between labs within a building.  In my experience,
the instrument vendors don't actually move the instruments, maybe some do.  The
service people I had basically did a quick checkout to verify working order,
then shut it down, disconnect, and do the reverse when the instrument arrives
at the new location.  I was responsible for the moving.  If something breaks
during the move then its possible the mover's liability insurance will cover
it.  That has never happened to me.  I've had movers transport triple quads,
ion traps (not orbitrap) HPLCs Biacore etc.  No problem.  Once, we purchased an
Agilent MALDI-TOF back in the late 1990s.  It was fairly small and on wheels.
It arrived on a truck wrapped simply in plastic.  The service engineer said
they had less damage when the delivery people could see the instrument through
the plastic wrap versus when it was crated and they could slam the crate
around.

Moving within a building with their smooth floors is easy if you have the
muscle power, and good carts, or a lift cart that can be positioned at the
bench height to slide heavy equipment off the bench to the cart at the same
height.  I've done this by myself to move an LTQ.  That instrument isn't that
big but wow is it heavy!  A student and I moved an LTQ Orbitrap "Classic" from
one floor to another.  It rolls fairly easy.  The vacuum pumps are moved
separately and that was harder than moving the Orbitrap.  WRT the Orbitrap, the
central electrode power supply is on the left side of the instrument toward the
bottom.  It is held on with rubber isolation mounts, which as rubber is prone
to do, degrade with time and so that power supply can drop down and then sit on
the cables that connect through the bottom of the power supply.  This will
happen just sitting still, but could be accelerated during moving.  So best to
check these mounts, or try to add some support to help it hang in place during
the move.  This should only be a problem on older instruments such as the
Classic etc that have been in the field for some time.

Moving between buildings, even if close, is best done via trucks because they
will provide a much smoother ride compared to rolling carts etc. down the
sidewalk.  Anything prone to vibrational damage should go on a truck no matter
how small.

If the path to the moving truck and back off at the new location is smooth,
then I would just push the orbitrap onto and off of the truck into the new
location.  However, the transitions from hallways to loading docks to trucks
usually isn't smooth.  So its best to have it palatized to allow the movers to
more "gently" traverse these transition points and use lifting equipment to
facilitate loading and off loading. Once on the truck and secured, it will feel
the same G-forces during the travel whether or not is palatized.  Possibly high
frequency vibrations would be reduced if palatized vs not.  You could get a
quote from Craters and Freighters if you don't want to have Thermo do it.

Finally, it probably wasn't your decision to move.  So it would be logical to
conclude that those who found it necessary to move should have a budget to pay
for the move.  You need the instruments to work at the new location.  So at
least in the case of the Orbitrap, if Thermo guarantees that it will work once
moved - if they move it - then pay for them to do just that. If your
institution balks a paying for that level of service, and it breaks in transit,
then your institution should pay for repairs, if the mover's liability
insurance doesn't.  For example, the central electrode power supply for the
Orbitrap "classic" costs about $22,000.

Rest of post

Cheers,

Brian
________________________________
From: ABRF Discussion Forum <email obscured>> on behalf of Bin Fang
<email obscured>>
Sent: Saturday, April 20, 2019 7:39 PM
To: ABRF Discussion List
Subject: Re: [ABRF Discussion Forum] Mass spec moving service

We did that 3 years ago. All bench top instruments should be easy to move.
Just take tons of pictures before you disconnect the components. Then you
can roll them on carts or benches with wheels. I'd be very scared to move
the old LTQ-orbitrap. That instrument is probably the only one I would ask
Thermo to move.





On Sat, Apr 20, 2019 at 6:58 PM Mawuenyega, Kwasi <email obscured>>
wrote:

> Hi Susie,
>
> My lab recently moved to a different building and I was in a similar
> situation. The solution I found (with a significant risk) was to hire a
> moving company to help with transportation. Professional movers are insured
> to cover damages up to a certain cost and they can tell you if your
> expensive instruments can be covered under their insurance. If there is
> anyone in your lab that knows how to take the instruments apart, that will
> save you a bunch of money. If the pumps and accessories are taken off, the
> MS itself can be rolled down the hall on carts or transported gently with a
> truck. There's no need to open the MS itself and tilting during
> transportation should be avoided at all cost. One Orbitrap Lumos, Fusion
> and triple quads were move and reassembled at the new location without a
> glitch. If you do not have anyone in-house to disassemble the instruments,
> then you will have to go with the vendors to be safe.
>
> I hope this helps.
>
> Kwasi
>
>
> -----Original Message-----
> From: ABRF Discussion Forum <email obscured>> On Behalf Of Susie
> Sent: Thursday, April 18, 2019 10:14 AM
> To: ABRF Discussion List <email obscured>>
> Subject: [ABRF Discussion Forum] Mass spec moving service
>
> Hi all:
> We are moving our orbit trap, LTQ, and GCMS from one building to a new one.
> The quotes we got from a vendor is very high. Any comments/thoughts/ideas
> for how to move?
> We moved the LTQ from one room to the other room by ourselves before. But
> now with a new building and an orbitrap, we kind of hope to get a better
> handle.
> Appreciate your inputs on this!
> Susie
>
> ――
> View topic http://list.abrf.org/r/topic/436Q6zl7fFpEPORjoTjkwE
> Leave group <email obscured>?Subject=Unsubscribe
>
>
> ________________________________
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ――
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>

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Hi Manfred
Sounds more like a book. Solid phase sequencing, peptide synthesis. 2d gels and
in gel digest and the trypsin and other digest sin all their flavours come to
mind
Gruß
Keith


Sent from my iPhone

> On 21 Apr 2019, at 3:01 am, Manfred@newtoncon <email obscured>> wrote:
>
> Hi,
>
> I am going to write a paper about the technical developments in Proteomics
and before, as protein analysis.
>
> Working in protein analysis for many years, as many of you, we went through
numerous technical and method developments – which disappeared quite fast and
never came back, like peptide ladder sequencing. And we spent time to follow
such developments and found out, they do not help at all. Thinking back – I
feel like a Proteomics tomb rider ☺
>
> For this I am looking for information about:
>
> Protein sequencers (ABI, Beckman, Millipore, Knauer, Shimadzu and – if
available – more) and C-terminal sequencers
>
> Amino acid analysers (ABI, HP, Beckman, LKB and who else)
>
> Preparative gel electrophoresis (ABI, Biorad, LKB……)
>
> Developments as the ABI plotter, the converted autosampler to a fraction
collector), static nano spray, and what else comes into mind
>
> Analytical developments: MudPIT, in-source decay, peptide-ladder sequencing,
PVDF plotting and sequencing….
>
> I will also include mass spectrometers, like the first MALDIs, PDMS (I used
one), early TSQs (had an API III, API 100), HPLC/FPLC equipment (still see some
LKBs around), electrophoresis (still active but also some older developments),
>
> And what else comes in your mind, please throw it on me and please use my
personal email: <email obscured>
>
> I am also looking for contributors – as co-authors, talked to some people and
they like the idea, also to prevent the newbies to make the same errors we went
through
>
> Many thanks
>
> Manfred
>
>
>
>
> ――
> View topic
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We did that 3 years ago. All bench top instruments should be easy to move.
Just take tons of pictures before you disconnect the components. Then you
can roll them on carts or benches with wheels. I'd be very scared to move
the old LTQ-orbitrap. That instrument is probably the only one I would ask
Thermo to move.





On Sat, Apr 20, 2019 at 6:58 PM Mawuenyega, Kwasi <email obscured>>
wrote:

Rest of post

> Hi Susie,
>
> My lab recently moved to a different building and I was in a similar
> situation. The solution I found (with a significant risk) was to hire a
> moving company to help with transportation. Professional movers are insured
> to cover damages up to a certain cost and they can tell you if your
> expensive instruments can be covered under their insurance. If there is
> anyone in your lab that knows how to take the instruments apart, that will
> save you a bunch of money. If the pumps and accessories are taken off, the
> MS itself can be rolled down the hall on carts or transported gently with a
> truck. There's no need to open the MS itself and tilting during
> transportation should be avoided at all cost. One Orbitrap Lumos, Fusion
> and triple quads were move and reassembled at the new location without a
> glitch. If you do not have anyone in-house to disassemble the instruments,
> then you will have to go with the vendors to be safe.
>
> I hope this helps.
>
> Kwasi
>
>
> -----Original Message-----
> From: ABRF Discussion Forum <email obscured>> On Behalf Of Susie
> Sent: Thursday, April 18, 2019 10:14 AM
> To: ABRF Discussion List <email obscured>>
> Subject: [ABRF Discussion Forum] Mass spec moving service
>
> Hi all:
> We are moving our orbit trap, LTQ, and GCMS from one building to a new one.
> The quotes we got from a vendor is very high. Any comments/thoughts/ideas
> for how to move?
> We moved the LTQ from one room to the other room by ourselves before. But
> now with a new building and an orbitrap, we kind of hope to get a better
> handle.
> Appreciate your inputs on this!
> Susie
>
> ――
> View topic http://list.abrf.org/r/topic/436Q6zl7fFpEPORjoTjkwE
> Leave group <email obscured>?Subject=Unsubscribe
>
>
> ________________________________
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ――
> View topic http://list.abrf.org/r/topic/biPdZIJ1TaoxeLqZuP6TG
> Leave group <email obscured>?Subject=Unsubscribe
>
>

Hi Susie,

My lab recently moved to a different building and I was in a similar situation.
The solution I found (with a significant risk) was to hire a moving company to
help with transportation. Professional movers are insured to cover damages up
to a certain cost and they can tell you if your expensive instruments can be
covered under their insurance. If there is anyone in your lab that knows how to
take the instruments apart, that will save you a bunch of money. If the pumps
and accessories are taken off, the MS itself can be rolled down the hall on
carts or transported gently with a truck. There's no need to open the MS itself
and tilting during transportation should be avoided at all cost. One Orbitrap
Lumos, Fusion and triple quads were move and reassembled at the new location
without a glitch. If you do not have anyone in-house to disassemble the
instruments, then you will have to go with the vendors to be safe.

I hope this helps.

Rest of post

Kwasi

-----Original Message-----
From: ABRF Discussion Forum <email obscured>> On Behalf Of Susie
Sent: Thursday, April 18, 2019 10:14 AM
To: ABRF Discussion List <email obscured>>
Subject: [ABRF Discussion Forum] Mass spec moving service

Hi all:
We are moving our orbit trap, LTQ, and GCMS from one building to a new one.
The quotes we got from a vendor is very high. Any comments/thoughts/ideas for
how to move?
We moved the LTQ from one room to the other room by ourselves before. But now
with a new building and an orbitrap, we kind of hope to get a better handle.
Appreciate your inputs on this!
Susie

――
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Leave group <email obscured>?Subject=Unsubscribe

________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.

Amino acid analysis: Waters PicoTag system (later AccQtag)
http://www.waters.com/waters/library.htm?cid=511436&lid=1524232&locale=en_US
<http://www.waters.com/waters/library.htm?cid=511436&lid=1524232&locale=en_US>
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547673/
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547673/>

If Steve Cohen (of Waters) is still on this list he may have more information
on this system.

Ümit

On 20Apr2019, at 13:49:38, Manfred@newtoncon <email obscured>> wrote:

Sorry forgot the AGILENT sequencer and the protein workstation
Manfred

Am 20.04.19, 19:00 schrieb "ABRF Discussion Forum im Auftrag von
Manfred@newtoncon" <email obscured> im Auftrag von <email obscured>>:

   Hi,

   I am going to write a paper about the technical developments in Proteomics
and before, as protein analysis.

   Working in protein analysis for many years, as many of you, we went through
numerous technical and method developments – which disappeared quite fast and
never came back, like peptide ladder sequencing. And we spent time to follow
such developments and found out, they do not help at all. Thinking back – I
feel like a Proteomics tomb rider ☺

   For this I am looking for information about:

   Protein sequencers (ABI, Beckman, Millipore, Knauer, Shimadzu and – if
available – more) and C-terminal sequencers

   Amino acid analysers (ABI, HP, Beckman, LKB and who else)

   Preparative gel electrophoresis (ABI, Biorad, LKB……)

   Developments as the ABI plotter, the converted autosampler to a fraction
collector), static nano spray, and what else comes into mind

   Analytical developments: MudPIT, in-source decay, peptide-ladder sequencing,
PVDF plotting and sequencing….

   I will also include mass spectrometers, like the first MALDIs, PDMS (I used
one), early TSQs (had an API III, API 100), HPLC/FPLC equipment (still see some
LKBs around), electrophoresis (still active but also some older developments),

   And what else comes in your mind, please throw it on me and please use my
personal email: <email obscured>

   I am also looking for contributors – as co-authors, talked to some people
and they like the idea, also to prevent the newbies to make the same errors we
went through

   Many thanks

   Manfred




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Rest of post





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