iiinova — where your digital self keeps evolving

Bini Ramachandran @itsbinir.bsky.social · 14/10/2026

Running a mass spec facility means having to mop down the water spilled from the backup chiller installed to maintain the room temperature as the Aircon decided it's not ime to breake down.. Especially since all these mishaps occur only in the after hours.. Life is beautiful.. #MassSpecMusings

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Bini Ramachandran @itsbinir.bsky.social · 20/08/2026

That's a frigging peptide spectrum match.. Playing with endogenous peptides on mass spec is funny.. 😊😊

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Bini Ramachandran @itsbinir.bsky.social · 16/02/2026

I have all these glycan specific fragments from a glycopeptide analysis.. Any software suggestions for identifying both the peptide and the attached glycan composition from such spectra?? Thanks very much.. #glycotime #TeamMassSpec

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Bini Ramachandran @itsbinir.bsky.social · 07/01/2026

Vanquish Duo as Neo Mono with EasySpray column setup.. Works quite alright.. Guess have to get uPAC to test the dual column setup at nano flow rate..

Chromatogram reproducibility for HeLa QC

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Bini Ramachandran @itsbinir.bsky.social · 26/12/2025

A slide from a presentation I gave in 2013 on mass spectrometry proteomics.. Ironically, still a relevant topic to include this slide as such in a talk I am preparing to give after the new year..

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Bini Ramachandran @itsbinir.bsky.social · 23/12/2025

Holidays started.. And the festive decor is on.. 🎉🎉#MassSpecHolidayDecor

Column emitter with a weird thing stuck on..

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Bini Ramachandran @itsbinir.bsky.social · 19/12/2025

Guess at which point I realized that the column heater is not connected.. I am very glad that this is the only boss-back-on-bench catastrophe so far.. The muscle memory from years of proteomics works still.. Thankfully, nothing got blown up.. yet.. 😂😂

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Bini Ramachandran @itsbinir.bsky.social · 21/11/2025

Even when the 96% of study sample contributors were females, the 4% males are the ones who get the mention!!! Wonder why can't the demography of the sample population be mentioned as 96% female or for better clarity as 96:4 female:male in the abstract.. Another instance of scientific gender bias??

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Bini Ramachandran @itsbinir.bsky.social · 24/09/2025

An international relocation doesn't mean packing up your entire life in a few bags to carry along with you anymore once you set up a base camp for yourself.. 😉😉

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Bini Ramachandran @itsbinir.bsky.social · 20/06/2025

A bunch of validated datasets analysed on a bunch of data analytics platforms with different workflow iterations to benchmark your analysis workflows against.. ProteoBench, a cool tool from EuBIC..

A screenshot from the ProteoBench webpage showing the steps for validation..

List of validated datasets available with ProteoBench

A graph comparing the quantified precursors with different data analytics platforms and iterations..

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Bini Ramachandran @itsbinir.bsky.social · 05/06/2025

Whats going on with MassIVE?? Issues with funding and/or resources?? All I wanted to do was to download the MAPS-MS data from Searle lab preprint and explore.. Authors, please deposit raw data in sustainable repositories..

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Bini Ramachandran @itsbinir.bsky.social · 29/05/2025

Maybe it's the difficulty to process changes at the first sight.. I do feel the panel design of Classic Astral is more appealing.. Hopefully, the new panel design will grow on me eventually.. 🤓🤓

Classic Orbitrap Astral mass spectrometry with a colourful panel..

New Orbitrap Astral Zoom mass spectrometer with a less colourful panel..

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Bini Ramachandran @itsbinir.bsky.social · 22/04/2025

CapLC proteomics at 1.5uL/min flow rate fared better in comparison to nanoLCs.. Not very surprising though.. Would have loved to see a comparison of chromatograms to assess gradient delay and active elution range..

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Bini Ramachandran @itsbinir.bsky.social · 21/04/2025

This is awesome.. A compilation of European proteomics labs on map- academic, industry, and service/core facility.. With details on contact info and a brief description on pop up.. Useful for everyone looking for European Proteomics Labs..

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Bini Ramachandran @itsbinir.bsky.social · 09/04/2025

This is a great figure compiling the quantitative aspects of those additional IDs retrieved by distinct data analytics tools.. Also, good to see the improved algorithm here reduces the CV of the common IDs..

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Bini Ramachandran @itsbinir.bsky.social · 16/03/2025

Such a beautiful example for fit-for-purpose mass spectrometry.. If the analyte is glycopeptides why waste resources by scanning the lower m/z ranges.. narrow window glycoDIA at 955-1655 mass range..

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Bini Ramachandran @itsbinir.bsky.social · 15/03/2025

SCP on Ascend fares better than TimsTof HT for a study that was not chasing to identify 5000 proteins per cell?? 🤔🤔 A nice study comparing the proteome level differences among native and drug-resistant prostrate cancer cells..

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Bini Ramachandran @itsbinir.bsky.social · 22/02/2025

Weekend proteomics upskilling exercise.. Getting more used to doing BLAST on Uniprot resources.. It's never too late to adapt to changes.. Even though it takes a little bit of getting used to.. www.uniprot.org/help/blast-s...

Uniprot blast search status display page

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Bini Ramachandran @itsbinir.bsky.social · 20/02/2025

TMT 11 reporter ions resolved (!) at MS2 level on an Ion Trap (above) and resolved at MS3 level on an Orbitrap (below) from the same precursor.. It's an intriguing comparison to draw... Data from one of the PD 3.2 training raw files..

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Bini Ramachandran @itsbinir.bsky.social · 03/02/2025

Guess ProteomicSky is collecting posts with those two emojis as well into the feed.. Not sure what those emojis mean though..

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Bini Ramachandran @itsbinir.bsky.social · 30/01/2025

It's a mixed feel when open access to news and perspective are also blocked by nature.. May be should feel happy that at the least it is not kept behind the paywall..

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Bini Ramachandran @itsbinir.bsky.social · 28/01/2025

Used tribrid for 10k GBP in auction?? 🤔🤔

Screenshot of Orbitrap Lumos listing from https://www.allsurplus.com/asset/5306/14233

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Bini Ramachandran @itsbinir.bsky.social · 28/01/2025

Titrating biotinylated probe and streptavidin conc to find the sweat spot is the key step in high throughput chemoproteomics workflow.. Especially balancing the target(s) specificity and yield.. Liked the heatmap depicting intensity of specific and nonspecific proteins from the pulldown..

Figure 2 from https://doi.org/10.1021/acs.jproteome.4c00696

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Bini Ramachandran @itsbinir.bsky.social · 15/01/2025

Why is the heatmap of protein quan by Olink appears monochromatic compared to neat plasma MS?? Is this how NPX readouts look like?? And why -ve readings on quan heatmap?? So many questions.. Being in a constantly evolving field means, being in a constantly learning mode. Ref in alt text and below.

Protein abundance heatmap of plasma proteins processed by Olink technology. From Supp.Fig.5 of https://www.biorxiv.org/content/10.1101/2025.01.08.632035v1

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Bini Ramachandran @itsbinir.bsky.social · 13/01/2025

Once proteomics goes beyond qualitative or quantitative cataloguing, fit-for-purpose clinical assays start emerging.. 53 protein MRM panel that works on regular UPLC and QQQ.. Targeted MS always for practical purposes...

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Bini Ramachandran @itsbinir.bsky.social · 03/01/2025

A model of the first MALDI-TOF mass spec I have ever used from decades back is available on eBay for <1000 USD now.. Payment can be done in installments over 6 months as well.. One for the collectors, huh.. 🤔🤨

A screenshot of eBay page listing shimadzu MALDI-TOF mass spec from 20 years ago for under 1000 USD..

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Bini Ramachandran @itsbinir.bsky.social · 28/12/2024

Is it natural to have the first thought as how the masses of these compounds will look in a mass spec and what its isotope patterns will be.. 🤔🤓 #MassSpecMusings..

Pictures of mineral stones displayed in the earth sciences section at Harvard museum..

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Bini Ramachandran @itsbinir.bsky.social · 20/12/2024

I was just thinking about the CE recalibration you were referring to in the PD training session early this month.. The shift in the ion ratio is consistent here as in the figure below.. Details are on alt text..

Stacked bar graph of fragment ion area, before upgrade.. 1st bar corresponds to library spectra..

Stacked bar graph of fragment ion area, after upgrade.. 1st bar corresponds to library spectra from before..

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Bini Ramachandran @itsbinir.bsky.social · 04/12/2024

Went down the rabbit hole and looked up the peptide IDs per minute records till 2017 after listening to the latest #TheProteomicsShow podcast. Wonder what this graph will look like with the updates from newer 100-300 SPD studies.. 🤓🤓 The is graph from www.cell.com/cell-systems...

Bar graph comparing number of peptides identified per min in publications till 2017. From Belker-Jensen et al, 2017 Cell Systems paper

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Bini Ramachandran @itsbinir.bsky.social · 23/11/2024

Also, regardless of the technology used, if all the proteins tested shows either positive or negative association with a trait, doesn't it make that correlation a little hard to comprehend??

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Bini Ramachandran @itsbinir.bsky.social · 08/01/2024

#MassSpecMondayArt.... Spectral recalibration has totally given up on this..

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Bini Ramachandran @itsbinir.bsky.social · 08/12/2023

FAIMS Vs No FAIMS.. Higher number of peptide IDs and lower TIC: FAIMS Lower number of peptide IDs and higher TIC: No FAIMS 100ng HeLa QC monitored on QCloud2..

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Bini Ramachandran @itsbinir.bsky.social · 22/11/2023

Chimerys detected more phosphosites than Spectronaut... Interesting...

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Bini Ramachandran @itsbinir.bsky.social · 21/11/2023

One of the downsides of AI appraisals is some of us, who barely pass as humans, failing these new tests to prove as one.. 😤😤 Apparently the pic on the right is the correct match for one on the left.. 😏

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Bini Ramachandran @itsbinir.bsky.social · 03/11/2023

Oh.. That's new.. Can read the article.. But can't download or print!!

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Bini Ramachandran @itsbinir.bsky.social · 29/10/2023

"In contrast to MS1, a reverse pattern was obtained for MS2 spectral acquisition (Fig. 2b). Here, the acquired MS2 scan numbers were higher for the Ranis specimens than GdC specimens (F = 161.19, p < 2e−16)" Emphasizing observations like this from MS data amuses me!! www.nature.com/articles/s41...

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Bini Ramachandran @itsbinir.bsky.social · 27/10/2023

It's interesting to see a significant jump in Prof. Et Al's citations since 2020.. Wonder what changed the trend.. More papers during covid or more covid papers.. 🤔🤔🤔

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Bini Ramachandran @itsbinir.bsky.social · 25/10/2023

My future toy.. I will have to work hard to not call it an A$$end every time.. 😉😉

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Bini Ramachandran @itsbinir.bsky.social · 17/10/2023

Yup. True. It's a pain. Guess they want to create a database on who shows interests in their applications. I would be curious to hear your take on this figure in the poster. Identifying different proteins from the same sample because of the difference in methods used is hard to get comfortable with

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Bini Ramachandran @itsbinir.bsky.social · 17/10/2023

Conclusions from Biognosys HUPO poster comparing Olink and their TrueDiscovery platform.. biognosys.com/resources/a-...

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Bini Ramachandran @itsbinir.bsky.social · 08/10/2023

"...disadvantages inevitably lead to [.....] severe underrepresentation of research from countries where English is not a primary language in English-language publications" "The manifold costs of being a non-native English speaker in science" journals.plos.org/plosbiology/...

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Bini Ramachandran @itsbinir.bsky.social · 03/10/2023

The former blue bird site is becoming a breeding nest for sp(c)ammers!!!! Looks like the end is near..

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Bini Ramachandran @itsbinir.bsky.social · 03/10/2023

Well... Today I like being on the old bird site.. That clarification is awesome..

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Bini Ramachandran @itsbinir.bsky.social · 30/09/2023

Blast from the past... Good(?) old days of plasma proteomics.. High abundant protein depletion using reusable chicken IgY ab matrix spin columns.. Look how reproducible each round of depletion was!!! Depleted and undepleted plasma in alternative lanes... circa 2011.. 🤓🤓

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Bini Ramachandran @itsbinir.bsky.social · 28/09/2023

BlueSky error messages are funny... What does this even mean, I wonder.. Are the servers crackling under the new SciSky influx?? 🤔🤔🤔

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Bini Ramachandran @itsbinir.bsky.social · 28/09/2023

Is it just me who gets triggered when the normalization factor goes near 2 in a TMT dataset?? 🤔🤔🤔 It is kind of an obsession to see it very close to 1..

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Bini Ramachandran @itsbinir.bsky.social · 26/09/2023

Guess it's subjective.. The screenshot is for 10 samples..

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