Searching FLASHDeconv .msalign in Toppic

[John Pavek]

Hello Dr. Liu,

I'm trying to search some .msalign files produced by FLASHDeconv in Toppic, but am getting the following error almost immediately upon starting the run (I've also included my parameters in case that's necessary, I have the "Missing MS1 feature file" button also checked) :

TopPIC 1.7.9

********************** Parameters **********************

Protein database file: C:/Users/MartyLabPC/Desktop/MartyLab/IsoDec/PXD019247/uniprotkb_proteome_UP000000625_2025_03_18.fasta

Spectrum file: C:/Users/MartyLabPC/Desktop/MartyLab/IsoDec/PXD019247/FLASHDeconv_msalign/20170105_L_MaD_ColC4_Ecoli20161108-10_01_ms2.msalign

Number of combined spectra: 1

Fragmentation method: ETD

Search type: TARGET

Fixed modifications BEGIN

Carbamidomethylation 57.0215 C

Fixed modifications END

Allowed N-terminal forms: NONE,NME,NME_ACETYLATION,M_ACETYLATION

Maximum number of unexpected modifications: 1

Maximum mass shift of modifications: 500 Da

Minimum mass shift of modifications: -500 Da

Spectrum-level cutoff type: EVALUE

Spectrum-level cutoff value: 0.01

Proteoform-level cutoff type: EVALUE

Proteoform-level cutoff value: 0.01

Error tolerance for matching masses: 10 ppm

Error tolerance for identifying PrSM clusters: 1.2 Da

Use TopFD feature file: True

E-value computation: Generating function

Localization with MIScore: False

Thread number: 4

Executable file directory: C:\Users\MartyLabPC\Desktop\MartyLab\toppic\toppic-windows-1.7.9\

Start time: Thu Mar 20 16:02:02 2025

Version: 1.7.9

********************** Parameters **********************

terminate called after throwing an instance of 'std::invalid_argument'

what(): stoi

ERROR Quit status: Crashed.

ERROR Quit code: 3.

I've attached one of the files. I'd appreciate any help you can provide!

Thanks,

John Pavek

[Liu, Xiaowen (Kevin)]

Hi, John,

 

FlashDeconv may not support TopPIC 1.7.9. You can test if TopPIC 1.6 or 1.5 can be used to search msalign files reported by FlashDeconv.

 

Best,

 

Xiaowen Liu

 

From: top-dow...@googlegroups.com <top-dow...@googlegroups.com> on behalf of John Pavek <jpa...@arizona.edu>
Date: Thursday, March 20, 2025 at 6:10 PM
To: TopPIC <top-dow...@googlegroups.com>
Subject: [ms-align-plus-pipeline] Searching FLASHDeconv .msalign in Toppic

External Sender. Be aware of links, attachments and requests.

--
You received this message because you are subscribed to the Google Groups "TopPIC" group.
To unsubscribe from this group and stop receiving emails from it, send an email to top-down-topp...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/top-down-toppic/576aee61-bca9-416e-97ed-1d7ccc4419a0n%40googlegroups.com.

[John Pavek]

Hello,

Is there somewhere that I can access a built version 1.5 or 1.6? I tried the link on the current download page, but it doesn't lead anywhere. I am running into issues building either version myself.

Thanks,

John

[liuxia...@gmail.com]

Hi, John, 

You can download TopPIC 1.6.5 from https://www.toppic.org/software/toppic_backup/toppic_1.6/register.html

Best, 

Xiaowen (Kevin)