Bini Ramachandran
@itsbinir.bsky.social
Mass Spectrometry/Proteomics nerd....
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.. 😉😉
September 24, 2025 at 8:11 AM
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.. 😉😉
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..
June 20, 2025 at 5:12 AM
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..
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..
June 5, 2025 at 11:08 AM
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..
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.. 🤓🤓
May 29, 2025 at 1:27 PM
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.. 🤓🤓
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..
April 22, 2025 at 1:13 PM
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..
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..
April 21, 2025 at 4:02 PM
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..
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..
April 9, 2025 at 5:57 AM
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..
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..
March 16, 2025 at 12:09 AM
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..
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..
A nice study comparing the proteome level differences among native and drug-resistant prostrate cancer cells..
March 15, 2025 at 11:49 PM
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..
A nice study comparing the proteome level differences among native and drug-resistant prostrate cancer cells..
Can't blame Canada for this..
March 5, 2025 at 7:01 PM
Can't blame Canada for this..
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...
www.uniprot.org/help/blast-s...
February 22, 2025 at 9:42 PM
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...
www.uniprot.org/help/blast-s...
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..
February 20, 2025 at 11:44 PM
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..
Guess ProteomicSky is collecting posts with those two emojis as well into the feed.. Not sure what those emojis mean though..
February 3, 2025 at 10:11 PM
Guess ProteomicSky is collecting posts with those two emojis as well into the feed.. Not sure what those emojis mean though..
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..
January 30, 2025 at 3:14 AM
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..
Used tribrid for 10k GBP in auction?? 🤔🤔
January 28, 2025 at 11:45 PM
Used tribrid for 10k GBP in auction?? 🤔🤔
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..
January 28, 2025 at 8:50 PM
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..
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.
Being in a constantly evolving field means, being in a constantly learning mode.
Ref in alt text and below.
January 15, 2025 at 8:37 PM
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.
Being in a constantly evolving field means, being in a constantly learning mode.
Ref in alt text and below.
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...
January 13, 2025 at 9:30 PM
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...
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.. 🤔🤨
January 3, 2025 at 9:04 PM
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.. 🤔🤨
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..
December 28, 2024 at 11:04 PM
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..
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..
December 20, 2024 at 1:10 AM
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..
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...
The is graph from www.cell.com/cell-systems...
December 4, 2024 at 9:47 PM
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...
The is graph from www.cell.com/cell-systems...
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??
November 23, 2024 at 9:47 PM
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??
#MassSpecMondayArt.... Spectral recalibration has totally given up on this..
January 8, 2024 at 7:02 PM
#MassSpecMondayArt.... Spectral recalibration has totally given up on this..