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Welcome to google group for MSstats!!

Here is the place to share your experiences, difficulties, solutions, and suggestions about the R-package, MSstats!

Applications for the May Institute 2025 are now open

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3/19/25

Upcoming Backwards-Incompatible Changes in MSstats 3.21 – Action Required

Correction: MSstatsSummarize will be replaced in favor of MSstatsSummarizeWithSingleCore On Wednesday

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Upcoming Backwards-Incompatible Changes in MSstats 3.21 – Action Required

Correction: MSstatsSummarize will be replaced in favor of MSstatsSummarizeWithSingleCore On Wednesday

3/19/25

Jan 2

Introduction to Statistics in R course - online, 19-22 January

Dear all, start the new year by building strong foundations in statistics with R! Our online course

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Introduction to Statistics in R course - online, 19-22 January

Dear all, start the new year by building strong foundations in statistics with R! Our online course

Jan 2

Roneldine Mesidor, Anthony Wu5

12/15/25

MSstats Big and selection of intensity column

Hi Anthony, It worked perfectly. Thank you so much! Roneldine On Wednesday, December 10, 2025 at 1:42

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MSstats Big and selection of intensity column

Hi Anthony, It worked perfectly. Thank you so much! Roneldine On Wednesday, December 10, 2025 at 1:42

12/15/25

Borja Belda Palazon, Mateusz Staniak8

12/3/25

Installation of MSstats in skyline failed

Hi, Thanks for your response. Mine is Windows but I will try to update to R 4.5.1. Best, Borja El

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Installation of MSstats in skyline failed

Hi, Thanks for your response. Mine is Windows but I will try to update to R 4.5.1. Best, Borja El

12/3/25

Sergio Ciordia, … Devon Kohler4

11/21/25

Evaluating MSstats Performance on Protein-Level vs PSM-Level Spectronaut Data

Hi Sergio, Filling these columns with arbitrary values is perfectly fine. They are just used to

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Evaluating MSstats Performance on Protein-Level vs PSM-Level Spectronaut Data

Hi Sergio, Filling these columns with arbitrary values is perfectly fine. They are just used to

11/21/25

Emilio Cirri, Anthony Wu2

11/6/25

Issues with SpectronauttoMSstatsFormat function

Hi Emilio, It sounds like you're using an old version of MSstats (our latest version if 4.18.0).

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Issues with SpectronauttoMSstatsFormat function

Hi Emilio, It sounds like you're using an old version of MSstats (our latest version if 4.18.0).

11/6/25

9/17/25

online course: R/Bioconductor for Mass Spectrometry and Proteomics - 17–19 November

Dear all, We are pleased to announce the 5th edition of the Physalia online course: R/Bioconductor

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online course: R/Bioconductor for Mass Spectrometry and Proteomics - 17–19 November

Dear all, We are pleased to announce the 5th edition of the Physalia online course: R/Bioconductor

9/17/25

PARTHIBAN PERIASAMY, … Mateusz Staniak4

9/8/25

Poor processing speed with 515 LC-MS/MS file with over 2000 protein during dataProcess step

Hi, Devon's advice concerns the dataProcess function from MSstats package. Arrow backend version

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Poor processing speed with 515 LC-MS/MS file with over 2000 protein during dataProcess step

Hi, Devon's advice concerns the dataProcess function from MSstats package. Arrow backend version

9/8/25

Clarissa Braccia, Anthony Wu3

9/8/25

Question about MSstatsPTM R package

Update on this thread: fractions for label free PTM experiments should now be enabled for MSstatsPTM.

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Question about MSstatsPTM R package

Update on this thread: fractions for label free PTM experiments should now be enabled for MSstatsPTM.

9/8/25

Lara Holoidovsky, Anthony Wu5

9/4/25

Missing replicates

Posting this update after private email discussions: I've determined that MSstats doesn't

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Missing replicates

Posting this update after private email discussions: I've determined that MSstats doesn't

9/4/25

Selim Bouaouina, Anthony Wu5

8/27/25

potential bug in .countMissingPercentage

Hi Tony, Thank you very much for your proposition, that's much appreciated. Due to a deadline I

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potential bug in .countMissingPercentage

Hi Tony, Thank you very much for your proposition, that's much appreciated. Due to a deadline I

8/27/25

Yunran, Anthony Wu3

8/25/25

Question on SpectronauttoMSstatsFormat

Posting a follow up question in case others have similar questions: "If I have donor 1-5 across

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Question on SpectronauttoMSstatsFormat

Posting a follow up question in case others have similar questions: "If I have donor 1-5 across

8/25/25

Marcel, … Anthony Wu11

7/29/25

DIA-NN 2.0 parquet file support

Changes to support DIANN 2.0 format should now be on bioconductor release 3.21 On Tuesday, July 15,

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DIA-NN 2.0 parquet file support

Changes to support DIANN 2.0 format should now be on bioconductor release 3.21 On Tuesday, July 15,

7/29/25

Chen Xi, Devon Kohler2

7/23/25

Data Format Conversion Inquiry for MSstats Compatibility

Hello, Unfortunately we do not currently have a converter for your output. I would recommend checking

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Data Format Conversion Inquiry for MSstats Compatibility

Hello, Unfortunately we do not currently have a converter for your output. I would recommend checking

7/23/25

ucl.c...@gmail.com, Anthony Wu2

7/11/25

Time-course study design annotation query

Hi Amandeep, You're on the right track here. I made adjustments to your annotation file and

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Time-course study design annotation query

Hi Amandeep, You're on the right track here. I made adjustments to your annotation file and

7/11/25

Eren Boybay, Anthony Wu3

7/10/25

dataProcess issue

Update on this thread: For those who may encounter this, you may have rows where the FragmentIon

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dataProcess issue

Update on this thread: For those who may encounter this, you may have rows where the FragmentIon

7/10/25

bw li, … Carlos Gonzalez9

6/27/25

Can't assign 4 names to a 0 column data.table

Hi Mateusz, Apologies my situation is not exactly like the issue above. For this, there is no

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Can't assign 4 names to a 0 column data.table

Hi Mateusz, Apologies my situation is not exactly like the issue above. For this, there is no

6/27/25

Debojyoti Pal, Anthony Wu5

6/24/25

Confused with the censoring and imputation options in MSStats

Thanks for the clarifications! On Monday, June 23, 2025 at 11:12:02 PM UTC+5:30 antho...@gmail.com

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Confused with the censoring and imputation options in MSStats

Thanks for the clarifications! On Monday, June 23, 2025 at 11:12:02 PM UTC+5:30 antho...@gmail.com

6/24/25

Marvin Altamia, Devon Kohler2

5/22/25

Data cleanup prior to file conversion?

Hi Marvin, The PD TMT converter does not currently filter out contaminants. I would recommend

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Data cleanup prior to file conversion?

Hi Marvin, The PD TMT converter does not currently filter out contaminants. I would recommend

5/22/25

Pratyush Routray, Anthony Wu5

5/20/25

trouble with Msstats

Here's the code: ``` library(readxl) library(MSstats) input = read_excel("Data_Pratyush.xlsx

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trouble with Msstats

Here's the code: ``` library(readxl) library(MSstats) input = read_excel("Data_Pratyush.xlsx

5/20/25

Sam Siljee, Mateusz Staniak26

5/19/25

Input for getWeightedProteinSummary

Hi, please use the current devel branch. The version is 0.99.15. Regarding the duplicates, I think I

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Input for getWeightedProteinSummary

Hi, please use the current devel branch. The version is 0.99.15. Regarding the duplicates, I think I

5/19/25

Jose Hyvärinen, Anthony Wu2

5/13/25

Protein summarization in MSstatsShiny crashes

Hi, Apologies for the delay as we recently finished teaching a short course these past 2 weeks. Have

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Protein summarization in MSstatsShiny crashes

Hi, Apologies for the delay as we recently finished teaching a short course these past 2 weeks. Have

5/13/25

Montoni Bass, … Sam Siljee3

4/30/25

Persistent Batch Effect

Hi Montoni, This might not be relevant to you, but I've noticed that including more details in

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Persistent Batch Effect

Hi Montoni, This might not be relevant to you, but I've noticed that including more details in

4/30/25

Jared Churko, Anthony Wu3

4/15/25

Error in eval(bysub, x, parent.frame()) : object 'Run' not found

Thanks Tony, Updating MSstatsTMT and replacing the "File ID" column name with "

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Error in eval(bysub, x, parent.frame()) : object 'Run' not found

Thanks Tony, Updating MSstatsTMT and replacing the "File ID" column name with "

4/15/25

Christian Schori, … Devon Kohler8

4/14/25

negative imputed values

Hi Jana, Are you getting any convergence warnings from the dataProcess function? It could be that the

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negative imputed values

Hi Jana, Are you getting any convergence warnings from the dataProcess function? It could be that the

4/14/25

Xiuyuan Chen, … Anthony Wu11

4/10/25

MSstatsTMT Converter Problem

Hi Xiuyuan, If you use MSstatsTMT, you can disable the normalisation function during the maxQuant

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MSstatsTMT Converter Problem

Hi Xiuyuan, If you use MSstatsTMT, you can disable the normalisation function during the maxQuant

4/10/25

Zachary Hutchins, Devon Kohler2

4/9/25

MSstatsTMT Global Median Normalization

Hi Zachary, The channels are equalized by subtracting the differences between medians so that the

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MSstatsTMT Global Median Normalization

Hi Zachary, The channels are equalized by subtracting the differences between medians so that the

4/9/25

Wing Man Ko, Anthony Wu5

4/8/25

error in converting Spectronaut 19 file to MSstats PTMFormat

Hi Tony, It works after adding the fragment headers. Thank you very much for your reminder! Best

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error in converting Spectronaut 19 file to MSstats PTMFormat

Hi Tony, It works after adding the fragment headers. Thank you very much for your reminder! Best

4/8/25

Alessandro Caioli, Anthony Wu3

4/3/25

Significant result from just 2 bioreplicates

Hi Tony, just wanted to thank you very much for your reply and your feedback, somehow I missed it and

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Significant result from just 2 bioreplicates

Hi Tony, just wanted to thank you very much for your reply and your feedback, somehow I missed it and

4/3/25

MATTHEW DING, Anthony Wu2

4/2/25

MSstatsPTM - some errors for Maxquant label-free datasets

Hi Matthew, Thank you for bringing this to our attention. Quick question - could you clarify which

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MSstatsPTM - some errors for Maxquant label-free datasets

Hi Matthew, Thank you for bringing this to our attention. Quick question - could you clarify which

4/2/25

Sam Siljee, Anthony Wu8

3/31/25

Issues in MSstatsPTM::dataSummarizationPTM_TMT

Hi Tony, I've been away on leave, so sorry for the delayed response. The solution of removing the

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Issues in MSstatsPTM::dataSummarizationPTM_TMT

Hi Tony, I've been away on leave, so sorry for the delayed response. The solution of removing the

3/31/25

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