【菜鳥博士學習】 File Conversion (Waters)總結
【菜鳥博士學習】 File Conversion (Waters)總結
菜鳥博士Caesar
File Conversion (Waters)
1. Introduction 1. 引言?
This page describes how you can convert raw data from Waters machines.
本頁描述如何轉換 Waters 機器的原始數(shù)據(jù)。
One of the most frequent questions from Waters users is if they can use MSe data for molecular networking. Bascially,?MSe data is not available for classical molecular networking workflow, because it is a type of data-independent acquisition method so does not include precursor ion information. However,?MSe data can be deconvoluted?(currently MS-DIAL is the proper software for it)?and applied to the FBMN workflow. You can find relevant information?here.
Waters 用戶最經(jīng)常提出的問題之一是，他們是否可以將 MSe 數(shù)據(jù)用于分子網(wǎng)絡。傳統(tǒng)的分子網(wǎng)絡工作流程基本上不能使用 MSe 數(shù)據(jù)，因為它是一種獨立于數(shù)據(jù)的采集方法，所以不包含前驅(qū)離子信息。然而，MSe 數(shù)據(jù)可以去卷積(目前 MS-DIAL 是適合它的軟件) ，并應用到 FBMN 工作流程。你可在此找到相關資料。
Currently, there are two different operating softwares for Waters machine, and they use entirely different file systems; thus, different data conversion pipelines are required.
目前，Waters 機器有兩種不同的操作軟件，它們使用完全不同的文件系統(tǒng); 因此，需要不同的數(shù)據(jù)轉換管道。
If you are using Waters machines operated by UNIFI software, see 2. How to convert UNIFI data for molecular networking
如果您使用的是使用 UNIFI 軟件操作的 Waters 機器，請參閱2. 如何將 UNIFI 數(shù)據(jù)轉換為分子網(wǎng)絡
If you have .Raw data files acquired by MassLynx software, see 3. How to convert Waters .Raw files to .mzML
如果您有 MassLynx 軟件獲取的.Raw 數(shù)據(jù)文件，請參閱3. 如何將 Waters. Raw 文件轉換為.mzML
2. How to convert UNIFI data for molecular networking 2. 如何將 UNIFI 數(shù)據(jù)轉換為分子網(wǎng)絡?
UNIFI keeps spectral data in Oracle database architecture, so you cannot get your raw data by simple copy and paste. Thus, as a first step of data conversion, you should export your data as MassLynx .Raw files. It can be done throught the file explorer, as shown below. Right-click on sample dataset will open the dropdown menu.
UNIFI 將光譜數(shù)據(jù)保存在 Oracle 數(shù)據(jù)庫架構中，因此不能通過簡單的復制和粘貼來獲得原始數(shù)據(jù)。因此，作為數(shù)據(jù)轉換的第一步，應該將數(shù)據(jù)導出為 MassLynx。原始文件?？梢酝ㄟ^文件瀏覽器完成，如下所示。右鍵單擊示例數(shù)據(jù)集將打開下拉菜單。
Supported GNPS Workflow for Waters UNIFI Machines
There is a bug in the current version of UNIFI, so if you try to export DDA data as .Raw, precursor ion m/z values will disappear. Thus, as we know, the only option for building molecular networks with UNIFI-operated system is the MSDIAL-FBMN pipeline with MSe data. If anyone knows how to convert DDA data from UNIFI into mzML, let ue know.
當前版本的 UNIFI 中有一個 bug，因此如果您嘗試將 DDA 數(shù)據(jù)導出為。原始的前驅(qū)離子 m/z 值將會消失。因此，我們知道，用 unifi 操作系統(tǒng)建立分子網(wǎng)絡的唯一選擇是具有 MSe 數(shù)據(jù)的 MSDIAL-FBMN 管道。如果有人知道如何將 DDA 數(shù)據(jù)從 UNIFI 轉換為 mzML，請告訴我們。
If you open the exported .Raw files using MassLynx or other softwares, you will find that m/z values are weird. This happens, because Lockspray correction will not be applied to the exported .Raw files. Thus, Lockspray correction will be the next step of the conversion.
如果你打開了出口。使用 MassLynx 或其他軟件的原始文件，您會發(fā)現(xiàn) m/z 值很奇怪。這種情況會發(fā)生，因為 Lockspray 修正將不適用于出口。原始文件。因此，鎖噴修正將是轉換的下一步。
The Lockspray correstion can be done while you centroid your data, using MassLynx. UNIFI do not have any option for centroid mode acquisition, so your exported data will be continuum. You can perform both of centroiding and Lockspray correction via 'Accurate Mass Measure' module of MassLynx. You can find it here:
鎖定噴霧相關可以做，而你的重心數(shù)據(jù)，使用 MassLynx。UNIFI 沒有任何選項的質(zhì)心模式獲取，所以你的導出數(shù)據(jù)將是連續(xù)的。你可以通過 MassLynx 的精確質(zhì)量測量模塊同時進行中心定位和 Lockspray 校正。你可以在這里找到:
Select files by double-clicking, or Operations > Select. If you want to move to other directory, close the module window, and open any datafile in MassLynx. Then the working directory will be changed.雙擊選擇文件，或操作 > 選擇。如果要移動到其他目錄，請關閉模塊窗口，并打開 MassLynx 中的任何數(shù)據(jù)文件。然后，工作目錄將被改變。
When files are selected, change the 'Process type' to 'Automatic Peak Detection'.選擇文件后，將“進程類型”更改為“自動峰值檢測”。
go to Parameters > Automatic Peak Detection Parameters, and select proper ion mode.點擊參數(shù) > 自動峰值檢測參數(shù)，選擇合適的離子模式。
Check the both options 'Set Peak Detection Paramters Automatically' and "perform Lock Mass Correction' on.檢查兩個選項“自動設置峰值檢測參數(shù)”和“執(zhí)行鎖定質(zhì)量校正”。
Put a proper Lock Mass m/z value into the "Lock Mass" window. If you are using leucine enkephalin, 556.2771 for positive ion mode, and 554.2615 for negative ion mode.在“鎖質(zhì)量”窗口中設置一個合適的鎖質(zhì)量 m/z 值。如果你使用亮氨酸腦啡肽，556.2771為正離子模式，554.2615為負離子模式。
Click 'OK' to close the parameter setting window, then click "Process".單擊“確定”關閉參數(shù)設置窗口，然后單擊“進程”。
Centroiding and Lock mass correction does not support multithreading, so this will take a long time. We recommend to run this on high-performanced workstations.
Centroiding 和 Lock mass correction 不支持多線程，所以這將花費很長時間。我們建議在高性能的工作站上運行這個程序。
When the processing is finished, you are ready to apply the files into the FBMN with MS-DIAL workflow. You can find detailed guideline?here.
當處理完成后，您就可以準備應用的文件到與 MS-DIAL 工作流程的 FBMN。你可以在這里找到詳細的指南。
3. How to convert Waters .Raw files to .mzML 3. 如何將 Waters. Raw 文件轉換為.mzML?
ProteoWizard msConvert has been updated several times, and the recent version resolved many problems known for Waters data conversion.
已經(jīng)更新了好幾次，最近的版本解決了 Waters 數(shù)據(jù)轉換的許多問題。
Here?is an updated version (with Proteowizard Release 3.0.21120) of the double-click converter we provided in our?guideline. Convert files with 'Double-Click_To-Convert_waters.bat'.
這是我們在指南中提供的雙擊轉換器的更新版本(具有 Proteowizard 版本3.0.21120)。用“雙擊 _ to-Convert _ waters.bat”轉換文件。
There is a known issue on precursor ion m/z values when Waters .Raw data are converted to .mzML. The precursor ion fields of MS/MS scans will have m/z values of quadrupole isolation windows, instead of accurate mass values. Unfortunately, we do not have any solution for this issue. Thus, if you will use converted .mzML files directly for classical MN, remember that every m/z values are drifted from the original data.
前兆離子的 m/z 值是一個已知的問題。原始數(shù)據(jù)被轉換為。mzML.MS/MS 掃描的前驅(qū)體離子場不再具有精確的質(zhì)量值，而是具有四極隔離窗的 m/z 值。不幸的是，我們對這個問題沒有任何解決辦法。因此，如果您將使用。mzML 文件直接為經(jīng)典的 MN，請記住，每個 m/z 值是從原始數(shù)據(jù)漂移。
If we will use the FBMN workflow, you can detour this issue by using .Raw files for MZmine processing, without converting them to .mzML files. However, the direct import of Waters .Raw into MZmine is not possible in MZmine ver 2.53 due to a bug; so try it with old releases.
如果我們將使用 FBMN 工作流，您可以繞道這個問題使用。用于 MZmine 處理的原始文件，無需將其轉換為。文件。然而，直接進口的水。在 MZmine 的2.53版本中，由于一個 bug，不可能使用 Raw 進入 MZmine; 因此，可以使用舊版本進行嘗試。
