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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!

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Mar 19

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

Mar 19

Lara Holoidovsky, Anthony Wu5

Sep 4

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

Sep 4

Selim Bouaouina, Anthony Wu5

Aug 27

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

Aug 27

Yunran, Anthony Wu3

Aug 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

Aug 25

Marcel, … Anthony Wu11

Jul 29

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,

Jul 29

Clarissa Braccia, Anthony Wu2

Jul 24

Question about MSstatsPTM R package

Hi Clarissa Would you be able to share your annotation file and a small subset of your maxQuant

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Question about MSstatsPTM R package

Hi Clarissa Would you be able to share your annotation file and a small subset of your maxQuant

Jul 24

Chen Xi, Devon Kohler2

Jul 23

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

Jul 23

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

Jul 11

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

Jul 11

Eren Boybay, Anthony Wu3

Jul 10

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

Jul 10

bw li, … Carlos Gonzalez9

Jun 27

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

Jun 27

Debojyoti Pal, Anthony Wu5

Jun 24

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

Jun 24

Marvin Altamia, Devon Kohler2

May 22

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

May 22

Pratyush Routray, Anthony Wu5

May 20

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

May 20

Sam Siljee, Mateusz Staniak26

May 19

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

May 19

Jose Hyvärinen, Anthony Wu2

May 13

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

May 13

Montoni Bass, … Sam Siljee3

Apr 30

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

Apr 30

Jared Churko, Anthony Wu3

Apr 15

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 "

Apr 15

Christian Schori, … Devon Kohler8

Apr 14

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

Apr 14

Xiuyuan Chen, … Anthony Wu11

Apr 10

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

Apr 10

Zachary Hutchins, Devon Kohler2

Apr 9

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

Apr 9

Wing Man Ko, Anthony Wu5

Apr 8

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

Apr 8

Alessandro Caioli, Anthony Wu3

Apr 3

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

Apr 3

MATTHEW DING, Anthony Wu2

Apr 2

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

Apr 2

Sam Siljee, Anthony Wu8

Mar 31

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

Mar 31

Sofia Farkona, … Anthony Wu29

Mar 24

Problem converting label-free MaxQuant data into MSstatsPTM format

Hello all I should give updates regarding the issues we have been experiencing here. The main two I

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Problem converting label-free MaxQuant data into MSstatsPTM format

Hello all I should give updates regarding the issues we have been experiencing here. The main two I

Mar 24

Yuen Ping Chong, Anthony Wu6

Mar 21

Error in dataProcess step

Yes that is correct, you should only select the peptides that are unique to proteins, ie use that

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Error in dataProcess step

Yes that is correct, you should only select the peptides that are unique to proteins, ie use that

Mar 21

Carlo Pecoraro, Sofia Farkona2

Mar 14

Mass Spectrometry and Proteomics in R/Bioconductor course - March 17-19

Hello there, this is extremely interesting. For people who are interested but have experiments during

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Mass Spectrometry and Proteomics in R/Bioconductor course - March 17-19

Hello there, this is extremely interesting. For people who are interested but have experiments during

Mar 14

Logan Johnson, Anthony Wu2

Feb 21

TMT unlabeled & 0 in Norm Channel

Hi, I'm not sure if I can answer your questions in one response as I'll need to follow up

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TMT unlabeled & 0 in Norm Channel

Hi, I'm not sure if I can answer your questions in one response as I'll need to follow up

Feb 21

Montoni Bass, Anthony Wu10

Feb 11

Annotation Issue

Dear Anthony, I was using a python script that was mistakenly ignoring some lines. Now I can see that

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Annotation Issue

Dear Anthony, I was using a python script that was mistakenly ignoring some lines. Now I can see that

Feb 11

mrudula mathew, Anthony Wu5

Feb 6

comparison matrix issue

Hi, Taking a look at your evidence file, the values in the `Raw file` column do not match with the

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comparison matrix issue

Hi, Taking a look at your evidence file, the values in the `Raw file` column do not match with the

Feb 6

Duong Trinh, Devon Kohler2

Feb 6

analyse proteins missing in 1 conditions

Hello, There proteins could be biologically relevant, but not statistics were possible due to them

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analyse proteins missing in 1 conditions

Hello, There proteins could be biologically relevant, but not statistics were possible due to them

Feb 6

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