Hi Dr. Chalk, Thank you for the lesson. Could you please let me know If Mascot and MaxQuant softwares are doing the same job? I see here you are using online spectral database for particular organism. However as I come across few years ago, MaxQuant use FASTA file and doesn’t use a spectral library. So, how does MaxQuant identify the peaks of particular protein? Thank you very much.
No, not really. I'm not expert on this but MaxQuant uses a different algorithm and is intended for quantitative proteomics experiments. These are discusssed here ua-cam.com/video/R3ltSKUgvBU/v-deo.html Mascot uses FASTA files. I'm not sure if MaxQuant uses spectral libraries. The database I use in this demonstration is SwissProt without taxonomic restriction. BW Rod
Hi Johachin, I've not used Scaffold. For RIME analysis I guess you would need a data anaysis program that can handle cross-linked proteins, so probably not Mascot. Rod
Thank you very much, valuable information, concise also. I was wondering if there is a way to include your own database (in this case a couple of engineered sequences + additional protein sequence for filling up the space of "own" database) in online mascot server, so you it pops up in the database(s) list in MS/MS Ions Search page?
Hello,
really good explanation, which helped me doing my Research with SARS-CoV-2 :)
Thank you for this!
Hi Lukas, you might enjoy this ua-cam.com/video/AkqTpNi47RY/v-deo.html
Rod
Thank you so much for this great explanation. Could I ask please if I used both Pepsin and Pancreatin, what I should choose on the search?
Hi Dr. Chalk, Thank you for the lesson. Could you please let me know If Mascot and MaxQuant softwares are doing the same job? I see here you are using online spectral database for particular organism. However as I come across few years ago, MaxQuant use FASTA file and doesn’t use a spectral library. So, how does MaxQuant identify the peaks of particular protein? Thank you very much.
No, not really. I'm not expert on this but MaxQuant uses a different algorithm and is intended for quantitative proteomics experiments. These are discusssed here ua-cam.com/video/R3ltSKUgvBU/v-deo.html Mascot uses FASTA files. I'm not sure if MaxQuant uses spectral libraries. The database I use in this demonstration is SwissProt without taxonomic restriction. BW Rod
@@rodchalk9945 Thank you very much for your kind reply Dr. Chalk.
Thank you Sir for this great video. It really helped me. I was wondering if you do also with scaffold for RIME analysis?Thanks
Hi Johachin, I've not used Scaffold. For RIME analysis I guess you would need a data anaysis program that can handle cross-linked proteins, so probably not Mascot.
Rod
Thank you very much, valuable information, concise also. I was wondering if there is a way to include your own database (in this case a couple of engineered sequences + additional protein sequence for filling up the space of "own" database) in online mascot server, so you it pops up in the database(s) list in MS/MS Ions Search page?
Sir How to interpret the MALDI tof results?
If your MALDI data is MSMS fragmentation data in .mgf format, the same applies
@@rodchalk9945 ok sir thank you so much
Hi DR. Is it posible that you give one of your files *.msg? Thanks in advance
Can you share how to perform sequence search in mascot
Hi Sachin, I'm not sure I understand your question. The video expalins how to do this. Can you be more specific?
Hlw Sir please send me unkown protien sequence sample file
please send me your email address
Hi Dr
can u help me to analyze my files?
hii Dr can you mail me unkown protein sequencing that you use At my email
send me your email and I will