H-T Lau
@htlau.bsky.social
A mass spec proteomics user in the CAR-T therapeutic space
Sadly Sciex doesn’t even want Skyline support
October 13, 2025 at 8:50 PM
Sadly Sciex doesn’t even want Skyline support
This is very nice. Thank you. I started with MaxQuant and always use narrow tolerance to search.
September 14, 2025 at 3:50 AM
This is very nice. Thank you. I started with MaxQuant and always use narrow tolerance to search.
Can you explain this? Are you guys talking about instrument settings or search settings?
September 11, 2025 at 10:12 PM
Can you explain this? Are you guys talking about instrument settings or search settings?
How many peaks across peak can you get from this kind of runs? I need to have a look at the data…
July 20, 2025 at 12:17 AM
How many peaks across peak can you get from this kind of runs? I need to have a look at the data…
I found it interesting that you were very kind when interview Nautilus’s founder. Perhaps the interview was not about their technology.
June 26, 2025 at 10:12 PM
I found it interesting that you were very kind when interview Nautilus’s founder. Perhaps the interview was not about their technology.
I think people will move away from mass spec with these platforms promising they can “quantify” thousands of protein in every run/sample.
March 15, 2025 at 3:59 PM
I think people will move away from mass spec with these platforms promising they can “quantify” thousands of protein in every run/sample.
I always wonder about this. Like those spatial proteomics platforms. Do they provide information saying they have verified every antibodies? I always feel suspicious about aptamers, probably because I liked the GDF11 story in 2010s so much and it turned out to be not reproducible…
February 27, 2025 at 12:15 AM
I always wonder about this. Like those spatial proteomics platforms. Do they provide information saying they have verified every antibodies? I always feel suspicious about aptamers, probably because I liked the GDF11 story in 2010s so much and it turned out to be not reproducible…
MS vendor - I don’t think so.
WhateverScan - Maybe?
WhateverScan - Maybe?
February 24, 2025 at 4:48 PM
MS vendor - I don’t think so.
WhateverScan - Maybe?
WhateverScan - Maybe?
They used to only have 3. I understand why your mind blown now. 🤯
March 4, 2024 at 2:16 PM
They used to only have 3. I understand why your mind blown now. 🤯
You should test those that you are interested in for different applications. I think they are cheap and last long enough (I stagetip my samples). Let me give you a email to get quote when I get back to work tomorrow.
March 3, 2024 at 5:57 PM
You should test those that you are interested in for different applications. I think they are cheap and last long enough (I stagetip my samples). Let me give you a email to get quote when I get back to work tomorrow.
I started with the 25 cm 75 mm ID and a 60 min run, then shortened to a 30 min gradient. I think I lost ~20% peptide counts, but not that much on protein. Then I talked to Bruker about fast gradient, they suggested me to use the 15x150. I think there isn’t much change in ID if I remember correctly
March 3, 2024 at 5:52 PM
I started with the 25 cm 75 mm ID and a 60 min run, then shortened to a 30 min gradient. I think I lost ~20% peptide counts, but not that much on protein. Then I talked to Bruker about fast gradient, they suggested me to use the 15x150. I think there isn’t much change in ID if I remember correctly
@proteomicsmarburg.bsky.social I have not tested them extensively. I mainly run whole cell lysates and I found them giving me similar peptide IDs. So I mainly use the 150um x 15cm for faster runs.
March 1, 2024 at 2:42 PM
@proteomicsmarburg.bsky.social I have not tested them extensively. I mainly run whole cell lysates and I found them giving me similar peptide IDs. So I mainly use the 150um x 15cm for faster runs.
I am still on this problem and Thermo is not fixing it for me. What a nightmare.
February 27, 2024 at 7:43 PM
I am still on this problem and Thermo is not fixing it for me. What a nightmare.
Have not tested nanoflow, but I think it will be worse.
January 5, 2024 at 2:45 AM
Have not tested nanoflow, but I think it will be worse.
2/ Peptides are eluting at different time because the path in the Flex is much longer. With 8 injections, the peak area CV centered at 5%. From the Neo, %CV centered at 15%. I am going to call Thermo.
January 5, 2024 at 2:45 AM
2/ Peptides are eluting at different time because the path in the Flex is much longer. With 8 injections, the peak area CV centered at 5%. From the Neo, %CV centered at 15%. I am going to call Thermo.
1/ OK, I am convinced that it is the Neo. I tracked the same enolase peptides using Skyline. All of those have good peak shape so integration is not an issue. Use the same PepMap 1 mm ID on both the Vanquish Flex and Neo, 50 uL/min at 40oC. Same gradient.
January 5, 2024 at 2:42 AM
1/ OK, I am convinced that it is the Neo. I tracked the same enolase peptides using Skyline. All of those have good peak shape so integration is not an issue. Use the same PepMap 1 mm ID on both the Vanquish Flex and Neo, 50 uL/min at 40oC. Same gradient.
I am doing more tests now. Digested some a protein, run it with a Vanquish Flex with Waters CSH column. The peptide peak areas are 5-6% CV. So I think I can rule out the mass spec at high flow condition.
Will do more tests and update.
Will do more tests and update.
December 21, 2023 at 1:04 AM
I am doing more tests now. Digested some a protein, run it with a Vanquish Flex with Waters CSH column. The peptide peak areas are 5-6% CV. So I think I can rule out the mass spec at high flow condition.
Will do more tests and update.
Will do more tests and update.
It is going up and down. I did 12 runs and there isn’t really a trend. The patterns of the peptides are also different. Like the first 5 can go up but the rest can go the other way…
December 21, 2023 at 1:00 AM
It is going up and down. I did 12 runs and there isn’t really a trend. The patterns of the peptides are also different. Like the first 5 can go up but the rest can go the other way…
No. It is going up and down
December 21, 2023 at 12:58 AM
No. It is going up and down
I injected from the same vial too.
December 20, 2023 at 1:23 AM
I injected from the same vial too.
I did a 7x eq volume. Direct injection, so no trap. I also started with the trap, but switched to direct injection because the intensity is much higher in direct injection.
December 20, 2023 at 1:20 AM
I did a 7x eq volume. Direct injection, so no trap. I also started with the trap, but switched to direct injection because the intensity is much higher in direct injection.
I use Waters total recovery vial. The standard is Pierce PRTC 5 pmol/uL. I diluted 1000x and injected 10 uL, so 50 fmol.
December 20, 2023 at 1:17 AM
I use Waters total recovery vial. The standard is Pierce PRTC 5 pmol/uL. I diluted 1000x and injected 10 uL, so 50 fmol.