Sam Payne
@byu_sam
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Bioinformatics professor at BYU. Interested in 'omics and awesome science.
Joined May 2018
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Well, it happened. I am reviewing a paper that is 100% plagiarized from my work. 🔥🔥
not 100% like "I'm certain it's plagiarized", but 100% like "every figure is from my public GitHub repo linked in the paper they are copying".
Editor friends - how does one review this?
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"Therefore, mRNA levels should not
be interpreted as the final output of gene expression.
Instead, it is more instructive to think of mRNAs as what
they mechanistically are: the templates for protein synthesis."
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Starting Monday with some gratitude
"Dear Professor Payne,
I have the privilege of the university's decision to grant you tenure and promote you to the rank of Professor"
Grateful to my amazing wife and family, to the students in bioinformatics, and to BYU.
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Amazing that I got asked to review it. like, lol did they know I would spot the fake? or are they just looking for people with single cell proteomics expertise?
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Pretty sure it's just a GPT recycle of our text with a direct copy of the figures.
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How many spare
#LEGO
pieces do we have? And how much spare time do we have over Christmas break? Enough to build a huge
#MillenniumFalcon
.
#HanAndTheAmazingTechnicolorSpaceship
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wonder if ChatGPT can just lift figures into a new PDF along with the garbled text?
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invaluable = more valuable
inaccurate = not more accurate.
Why, english? Why?
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@slavov_n
All of them. That was my student’s talk in Boston, in general the correlation between protein and transcript across all genes in healthy tissue is zero. This is not new. There’s a Sunny Xie Science paper from 2012 which shows this in single living cells.
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#TeamMassSpec
- My undergrads have created some tutorials for learning mass spec from a computational point of view (not a chemistry point of view). If you're looking for some
#FridayFun
, take a look and let me know what you think.
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@DalalSci
@SaraTetraDec
everyone starts their research career somewhere. Post-docs are the most skilled and most senior. so often PIs want just those with high skill. But everyone starts somewhere. And those with primarily undergrad labs are helping all the future post-docs and PIs get a start
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I especially loved the philosophical discussion of “what is gene expression?” And how this was cheapened by our use of a proxy shortcut -mRNA abundance.
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Is it okay to cite
#TeamMassSpec
in a paper acknowledgements? I mean, i get a lot of help here.
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@HikesWithDogs00
the editor has been very terse. I have no idea what they use (but I asked). I doubt it was flagged, because why would you send it out for review if you thought it was plagiarized
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As
#TeamMassSpec
gets excited for
@asmsnews
conference next week, my gentle reminder that the presenters are people too. Many of them are students (even undergrads) and don't need your pithy comments or stern rejection of their work.
#BeKind
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my first mis-citation, - citing my paper with the exact opposite conclusion.
"and throughout literature mRNA abundance has been taken as an effective proxy for protein expression [3–5]"
I'm citation 3, and my entire paper is about how mRNA is a terrible proxy for protein.
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My paper -
My Fig - Their Fig (not sure what "ABC calculation" means)
Well, it happened. I am reviewing a paper that is 100% plagiarized from my work. 🔥🔥
not 100% like "I'm certain it's plagiarized", but 100% like "every figure is from my public GitHub repo linked in the paper they are copying".
Editor friends - how does one review this?
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4K
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#NewPaper
. Just out in
@molcellprot
is our review of the computational challenges for single cell proteomics. Hannah and I analyzed the primary data analysis steps in peptide/protein id/quant.
#TeamMassSpec
, there is lots to do.
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#newPaper
on
@biorxivpreprint
today. With the rise of single cell proteomics, we wanted to understand which tools worked the best. So we did a bake-off! Two big messages
1. several tools work very well
2. things get much better with posthoc rescoring
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This beautifully written paper is by
@SelbachLab
. I highly recommend reading the whole thing as it carefully describes the mRNA and protein relationship. Specifically what the central dogma does and does not imply.
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#NewPaper
out on single cell proteomics of human ALS neurons. Great collaboration with
@biogen
and
@ryankellybyu
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Dear
#scitwitter
,
Don't title your paper "proteomic evidence..." and only have transcriptomics data. Proteins and mRNA are different.
Thx
A proteomics scientist
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@mjmaccoss
super terse. 'thx for the help. we rejected'
But I was pretty specific about their lack of checks and a serious need for following up. I'm not sure if he heard that part.
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#NewPaper
Our
#CPTAC
proteogenomics data API is finally out. Huge success for my students, with Caleb leading the way.
Thread below on why this is so important⬇️
#OpenData
#sharingiscaring
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Our work on single cell proteomics data analysis is out!! I’ll teeet a ritual after the holidays. 🎄
Researchers characterize the differences between single-cell spectra and bulk spectra by examining fundamental spectral features that are likely to affect peptide identification performance at low levels of input sample material.
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New Preprint - generalized FDR model for
#lipidomics
. Borrows ideas from
#proteomics
FDR. trying to help our
#metabolomics
peers have the same level of confidence in their identifications. the PeptideProphet and TargetDecoy models revolutionized proteomics
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Perspective matters
A student asked me why
#MSFragger
open searches take so long. I asked how long. He said 10 minutes. 😂
When we published our open search in 2008 it was a huge achievement that it took hours instead of days.
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Biden signs executive order officially recognizing that proteins are the functional molecules in cells. Encourages scientists to actually measure proteins and not use RNA as a proxy.
🚨BREAKING:
Biden signs executive order banning validation of proteomic results by western blot
#TeamMassSpec
#proteomics
#academicTwitter
#phdchat
@PhDVoice
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#NewPaper
alert.
#TeamMassSpec
, we just finished our review of the computational challenges for single cell proteomics.
@biorxivpreprint
won't handle a review, so here's a link to the pdf -
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@GarciaLabMS
I'm always surprised that this is not universal. It should be part of onboarding for all faculty and biotech scientists.
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#TeamMassSpec
- Please put the PRIDE/MassIVE accession in your Methods section. Preferably in the part that describes your LC-MS conditions. Please do not put it at the end in a footnote, or in a citation, or somewhere else obscure.
Make it easy to find your data
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"Although many methods exist for imputing missing values in proteomics data, in practice, the most commonly used methods are among the worst performing."
Unfortunate, but true.
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#Bioinformatics
tweeps. There are many options for pathway enrichment. What to do when they disagree?
Reactome: pathway X is the most significant in all data.
GSEA: 😴😴 pathway X is so uninteresting. I don’t even want to give it a score.
Me: 🤔😭🤫
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Been helping my kids with algebra, geometry, French, US govt, literature, etc. for like 8 months now. Finally one of them asks “dad. Are you able to help with my Python program?”
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Do people put their exact sample prep protocol in a manuscript as supp docs? I mean the step by step numbered/bullet instruction sheet that we follow. That seems easier than trying to make a prose paragraph out of the protocol doc that I already have.
#ScienceTwitter
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I have a crazy idea, and Friday afternoon seems like the right time to unleash this.
I want to gather best practices in proteomics data analysis. Teaching things like FDR filtering, normalization, differential quant. We explain caveats, etc.
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Paper just out in
@JProteomeRes
with
@OmicsPNNL
@coldfire79
@GrmyClair
@P3p7id3
. Individual proteome variability and
#MachineLearning
. It is
#openscience
with a
@ProjectJupyter
notebook for each figure. all data and code at
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biggest thing that contributes to my imposter syndrome is seeing new papers that look like ideas I had years ago but abandoned because the results were not cool enough. Somehow when other people do it, it is cool enough to get into
#CellScienceNature
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i keep recommending people to join
#TeamMassSpec
on twitter. They think it's strange, but I find this online community super valuable. Thanks team
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Just found this paper that says a typical CV formula is wrong if your data has been log transformed. All mass spec quant is log transformed. Do people use this complex formula or the simpler stdev/mean?
#proteomics
#noJudgementStatsHelp
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#teamMassSpec
let's start classifying MS/MS id algorithms as '1st gen' or '2nd gen'.
1st gen = a theoretical spectrum has peaks of equal magnitude
2nd gen = peak intensity is a native and critical part of the scoring metric
Also - let's get more 2nd gen software
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Dear grad students
You matter to your PI. They strive for your success.
You need something - ask
You struggling - ask for help.
A good PI will help you succeed.
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Simple suggestions to improve
#reproducibility
#transparency
#openscience
1. figures made with code
2. both code and input files accessible, e.g.
@github
3. figure legends and methods prominently cite the repository
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A 🧵 on Hannah's awesome new paper for
#SingleCellProteomics
.
There has been a ton of work improving the sample prep, LC and MS. But relatively little for the evaluation or improvement of computational tools. Here we look at PSM identification, the foundation of proteomics
Researchers characterize the differences between single-cell spectra and bulk spectra by examining fundamental spectral features that are likely to affect peptide identification performance at low levels of input sample material.
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My career trajectory changed when a college professor invited me to join his lab and do research. At the time I did not really know about 'research'.
As a PI, I now try and reach out and invite people to join the lab. Fantastic people are out there.
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What are people using for DIA data analysis these days? I feel like I need to catch up.
#TeamMassSpec
bonus points if you link to the paper describing the tool.
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Want to play around with
#COVID
ー19 data?
Want the official data from
@JohnsHopkinsSPH
?
Looking for the absolute easiest way to get that data?
if you
>pip install covid19pandas
then you can 👇 and get data immediately as
#pandas
#dataframes
.
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wow. This is a fantastic resource for undergraduates wishing to apply for grad school. Although it is written for the Genome Sciences at UW, it contains very good advice for general grad school applications.
Interested in applying for PhD programs at
@uwgenome
and similar departments? We’ve added new info to our website on how to become a competitive candidate, write a compelling application, and register for zoom info sessions:
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#NewPaper
from the lab. improved access to cancer proteogenomic data through a data API. greatly simplifies collaborative research and improves transparency.
#CPTAC
#OpenScience
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Excited to announce a new collaboration with
@Smith_Chem_Wisc
and
@thabangh
on
#singlecellproteomics
through
@cziscience
. Looking forward to bringing improved quantitative awesomeness to SCP and
#TeamMassSpec
We’re excited to announce 20 new Data Insights grantees addressing challenges in
#SingleCell
biology by:
🔹Integrating data sets to understand cell functions that regulate health + disease
🔹Applying
#ML
methods to the analysis of complex data sets
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#falseAlarm
. I just saw an email pop up in my inbox that said “manuscript accepted” I was so excited. Then I opened the email and found out it was someone else’s manuscript that I was the reviewer on.
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#TeamMassSpec
- what do we think about FDR probability estimates? If an algorithm says that it's 1% but you look deep into the PSM ids and count decoys and find out that it's not 1%.
I've been benchmarking algorithms and there is real variability here. both above/below estimate.
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Just your daily reminder that the vaccine for COVID is safe and effective
US covid cases: 28 million
US covid deaths: 485,000
US vaccines: 52 million
US deaths from vaccine: ZERO
If someone is telling you about the vaccine being dangerous - they are wrong.
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Welcome incoming class! There are lots of professors here on Twitter. We are all here to support you.
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@TrumanLab
@LisaMariaN91
As a student I avoided these labs. It was a very conscious choice. As a manager in biotech and now academic PI, I tell my peers to stop this. Stop thinking of other people as a commodity, as a vehicle for your work’s advancement
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To help raise the visibility of kindness, I want to thank a reviewer from
@molcellprot
. In addition to saying that the revision satisfied their concerns, they wrote a beautiful and generous paragraph about how they believe the paper would have a positive impact. Thx.
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My dad passed away last week after a 25 year struggle with
#Leukemia
,
#lymphoma
, multiple metastases and recurrences. He was an example of purpose, devotion, love and kindness.
#hometoheaven
#reunion
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Office decoration has officially started. Thanks
@BioDataGanache
for the art!
#alreadygettingcompliments
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#CPTAC
pan-cancer papers! Great work by a huge team, identifying the phenotypic consequences of mutation across 10 cancer types. Proteogenomics FTW!
Driver mutations:
Protein modifications:
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@GarciaLabMS
@CWolberger
@NIH
faculty that understand the difference between 'training' and 'more labor'. A post-doc is supposed to be training moment, not just skilled hands cranking experiments for the PIs papers.
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#TeamMassSpec
, we are losing ground fast to other technologies for proteomics. It is clear that what we need is much improved throughput and easier data analysis.
Organ aging signatures in the plasma proteome track health and disease | Nature
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#TeamMassSpec
. looking at DIA-NN today to try and learn about library-free methods. The manuscript says that it takes a spectrum library or can operate without. So is it always library-free, or just optionally library free?
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#TeamMassSpec
In optimizing LC gradients, I've heard recommendations on the number of measurements across an ion's elution in order to get good quantification (like 7 data points at full-width half-max). Are there any pubs about this?
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"Because proteins perform the overwhelming majority of biological processes, the results from transcriptomics data might be differentially relevant to biological processes based on how well they predict protein level."
Can I get an Amen!
@LauLabColorado
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Surprising only to the transcriptomics crowd. Not to
#TeamMassSpec
.
mRNA abundance does not predict protein abundance
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#NewPaper
Our exploration of a critical question for
#singlecellproteomics
. How many cells do you have to measure?
Collaboration with
@ryankellybyu
and
@biogen
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What's the difference between Chemical Biology and Biochemistry? Like am I going to see my community re-brand in a few years from bioinformatics to inforbiologics?
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How do you politely say “the reviewer is wrong. I’m sorry my text was unclear. I hope the revisions make this point clear.”
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@MicrobiomDigest
@lgatt0
@BioMickWatson
@PubPeer
@RetractionWatch
We took a stab at making a tool to detect fraud in omics data tables
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So excited to release our
#proteomics
de novo identification tool Kaiko.
#DeepLearning
with enough data (5 million spectra) helped us create an amazing tool for proteomics when you don't have a genome.
@OmicsPNNL
and huge kudos to
@coldfire79
.
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#TeamMassSpec
, how can we fix this?
"Although meta-analyses are common in other omics fields, leveraging of multiple published datasets to overcome statistical power limitations and lack of reproducibility has been neglected in the proteomics field."
-
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reviewing a paper that has "Single-cell proteomics has attracted a lot of attention in recent years because it offers more functional relevance than single-cell transcriptomics."
Sweet music to my ears
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Excited to post an update to our de novo
#proteomics
tool, now incorporated into a metaproteomics tool for direct identification of species in the data - without sequencing data. Great work by
@coldfire79
@BurnumJohnson
and the
@omicspnnl
team
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@RitaSin17562778
Or people are realizing just how important proper support is during difficult times. I got married as an undergrad. Best decision ever. Was essential to my mental health and success as a graduate student
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@strokelab
I'm not the doxing type. Also, it's not clear to me that the authors or institution are real (the internet can be fuzzy). So I'm perplexed at who is ultimately responsible.
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