Tejas Gandhi

Developing software for proteomics data analysis at Biognosys

[Tejas Gandhi @JustATejas]

@DemichevLab @GeiszlerDaniel @byu_sam Hi Vadim, thanks for your answer. In this case, it did contain as they were using a booster channel with e.coli spiked in and calculating FPR on only input samples with no e.coli. Why I was a bit surprised. We can take this offline.

[Tejas Gandhi @JustATejas]

@DemichevLab @GeiszlerDaniel @byu_sam Hi Vadim, in a recent publication, I was confused that authors did not need any local FDR filter in dia-nn to control local entrapment ratio. I found that interesting as it breaks theory. Can you please explain what exactly is lib.q.value and how it is used in the second pass?

[Tejas Gandhi @JustATejas]

@byu_sam @cardiotrends @Maccoss During the targeted analysis with the lib generated from all samples, each sample is treated independently except for post-scoring processes such as protein inference, normalization, and global FDR. For controlling local FDR, most DIA software provide run level FDR controls.

[Tejas Gandhi @JustATejas]

@byu_sam @cardiotrends @Maccoss The lib in a "library free" analysis is generated from all the samples in a 1st pass. The classical targeted analysis is then done using this lib which is sometimes referred as "MBR", quite different from DDA. Can think of first pass as using DDA on a pooled sample for lib.

[Tejas Gandhi @JustATejas]

@neely615 @biognosys Come on over!

[Tejas Gandhi @JustATejas]

DIA workshop starting soon in room 210ABC #ASMS2024

[Tejas Gandhi @JustATejas]

@ItsBiniR hmm apparently, I can't private message. Twitter newb here. Think you can figure out my email? I am from Biognosys, you can also write to support.

[Tejas Gandhi @JustATejas]

@ItsBiniR Hey Bini, we can chat. I will send you my email to schedule.

[Biognosys @biognosys]

Prepare for lift-off! Spectronaut 19 is coming on June 4 🚀👀 To learn all about the new version, join us for our breakfast seminar at #ASMS2024 🎉🍳☕Learn more and register here: https://t.co/1dxy3og3FD

[Tejas Gandhi @JustATejas]

@Yanshen73854711 Hope to see you at the conference!

[Tejas Gandhi @JustATejas]

@AOri_lab @LeibnizFLI @ERC_Research Excellent news and well deserved. Congratulations!!

[Tejas Gandhi @JustATejas]

@UCDProteomics IM overview plot in SN can be helpful. I have found couple of bad runs like this in the past (ion cloud shifted out of targeted windows), but it is rare.

[Tejas Gandhi @JustATejas]

@AJ_Brenes No problem. We will look into adding a message directly in Spectronaut with one of the updates. Thanks for your feedback.

[Tejas Gandhi @JustATejas]

@AOri_lab @OliverMBernhar1 Thanks for your valuable input during the development!

[Tejas Gandhi @JustATejas]

@AJ_Brenes @OliverMBernhar1 @biognosys You can find all the information about the new release here, including a link to detailed release notes: https://t.co/kV27iLM8sx

[Tejas Gandhi @JustATejas]

@UCDProteomics @OliverMBernhar1 Hey Brett, I expect you will appreciate the new ion mobilogram plot :)

[Tejas Gandhi @JustATejas]

@BobbyKlaus3 @lkpino @SkylineUW We published pulsed Silac data using Spectronaut last year. The supplementary has a step-by-step protocol for processing such data within Spectronaut. https://t.co/q4xWwZRuFr