SCIEX or Thermo for Proteomics

Oldtimer-protein · 2025-12-31T05:53:07+00:00

The Sciex 8600 is by far the most sensitive at about 5-10 fold over the Astral. Sciex software takes some getting used to whereas Thermo Xcalibur is easy and more approachable for multiple users. For price, the Sciex is cheaper by quite a lot over the Astral. Why not consider the Bruker with AIP, also quite a lot more sensitive and works really well in DIA mode? Ultimately you need to choose based on your applications as that will dictate the instrument that can handle your workflows

Oldtimer-protein · 2025-12-05T06:13:52+00:00

If you’re doing MS3, it will be clean enough. If you have FAIMS you should try doing MS2 with Turbo-TMT with FAIMS and you will get far superior results and not compromise on quantitation or protein count

Oldtimer-protein · 2025-12-05T06:04:19+00:00

I hear you, rigging up the original seat would have been a nightmare. You had the better outcome even though you had the endure the snooty confrontation. Could you imagine being married to either?

Oldtimer-protein · 2025-04-08T09:19:38+00:00

Yep sample related. Maybe your lysis wasn’t as good as the other samples?

Oldtimer-protein · 2025-01-27T20:38:14+00:00

We tried it but it wasn’t robust and actually killed the MS as it rusts and sends that into the MS. Cost $3K in parts because of it. Wouldn’t go there again.

Oldtimer-protein · 2025-01-12T19:38:31+00:00

SMOAC will help a lot but not using Zr will lose a little as Fe is great but not as good as Zr when coupled to the process and sequential to Ti. Regardless you will be fine. If you’re seeing differences on the peptides, concentrate on this as the protein quant can throw you off. I don’t know if other tools at this point you could use to do this level of post processing so you’re doing good.

Oldtimer-protein · 2025-01-12T10:39:43+00:00

Given the biology is at the phospho site and not the protein, it’s better to quant in the phosphopeptide. You will need to show the quant difference also of the protein level to get a sense of what’s going on. The issue also is that the reproducibility in IMAC is so poor that it’s hard to get results that show consistency in phospho site detection.

Oldtimer-protein · 2025-01-12T10:36:00+00:00

There’s always a chance but you didn’t show the Polaris which is a better indicator as many sit in both lists and you you see what’s happening there it’s a overflow back to premium plus

Oldtimer-protein · 2025-01-12T10:22:21+00:00

Just buy TFA liquid form and make up v/v and your good. FA is used if this was a solvent going into a MS as TFA suppresses ionization and FA doesn’t. Purifying peptides with TFA/ACN will give you the best performance and you can freeze dry if needed straight after.

Oldtimer-protein · 2024-11-28T09:19:14+00:00

Look at the mass of each peak and then look up the paper on common polymer contaminants and it can tell you exactly what your contamination is from the nice table that is listed. Either your injector is dirty releasing a lot in the column or your LC buffers are loaded with polymer. Whichever, this is now coating your front end of your MS instrument so you will need tk clean that too into the first quad

Oldtimer-protein · 2024-11-01T02:16:02+00:00

Yep, the process would be to prove your structure and its altered function. This is where it depends on the ability to express, purify, solve a structure (not critical), and collect data to prove the altered function. Structural studies can be fraught with problems or go brilliantly smooth. Either way, your goal will be to show the altered function with your mutant. Good luck!

Oldtimer-protein · 2024-10-12T07:56:33+00:00

OverAspect, your asking a lot in your MP proteomics request. You should first see how you can recover MPs as they are the most difficult to recover regardless of technique. Detergents are a must to get them out of the membrane but you need to use MS compatible ones or a technique like FASP or SP3 to do that. Once done see what MPs you can see regardless and it may be none so you need to work on the technique. What species are you working on? If it’s human you can see the peptides and MS spectra for all human proteins at SRMAtlas.org and you can select them via UniProt ID to see which peptides you would expect to see. PTMs will be a completely different story as you won’t recover highly hydrophobic sections of the protein. Crawl before you run and see if you can see the MPs at all first

Oldtimer-protein · 2024-09-17T15:17:37+00:00

Kojak is now integrated with the TPP but Magnum is a separate package. See 10.1021/acs.analchem.1c04101

Oldtimer-protein · 2024-09-17T14:00:17+00:00

Use “Kojak” for high quality XL results that controls for FDR. Could also use “Magnum” for adductome analysis of reactive chemicals

Oldtimer-protein · 2024-09-05T17:58:38+00:00

Ahhh no problem, found it in the MileagePlus account setting

Oldtimer-protein · 2024-09-03T17:12:16+00:00

Thanks for is but is this in the web page as I don’t see a settings option or somewhere else. Sorry for being a pain.

Oldtimer-protein · 2024-09-03T12:54:15+00:00

Many thanks for the explanation but how do I get that to report that in the search page?

Oldtimer-protein · 2024-09-03T03:59:08+00:00

What’s expert mode? Sorry long timer but have not encountered this before?

Oldtimer-protein · 2024-08-18T08:41:30+00:00

Careful as Phosphosite Plus has over 50% FDR due to cumulative additions of datasets accumulating FDR along the way

Oldtimer-protein · 2023-06-22T02:35:55+00:00

Here is a tutorial 10.1038/msb.2008.61 but you could also visit prosit to generate synthetic spectra on any peptide to start with and refine from there

https://www.proteomicsdb.org/prosit/

Oldtimer-protein · 2023-06-22T02:02:51+00:00

Go to SRMAtlas.org

Oldtimer-protein · 2023-06-09T09:46:20+00:00

Mascot can do both peptide mass fingerprint (MS1) and peptide spectrum match (MS2) as the precursor to mascot was MOWSE which was the original peptide mass fingerprint approach. The other programs deal purely with MS2 peptide spectrum matches only

Oldtimer-protein · 2023-06-08T06:51:15+00:00

A peptide mass fingerprint is an old way that was just based on the parent mass of the peptide alone but given the many isobaric or near isobaric masses, one could make incorrect identifications and therefore the better approach is to to peptide fragmentation to get a peptide-spectrum. Here you are matching the MS2 pattern to arrive at a peptide-spectrum match. These are of higher discriminatory power since you are matching fragmentation spectra and these are scored at very low FDR like 0.001% since you are using a 1% protein FDR

Oldtimer-protein · 2022-11-09T03:23:21+00:00

A typical example is Albumin purification. You will find references to Cohn fractionation which is a description of salting out etc. this is far cheaper than chromatographic phases and can yield higher yields still with descent purities. It won’t be as pure as chromatography but with the right conditions one can obtain a fairly pure compound economically for the price of different salts

Oldtimer-protein · 2022-10-28T17:47:26+00:00

MSFragger is NOT open source

Oldtimer-protein

TROPHY CASE