Error when using ProgenesistoMSstatsFormat()

vjmall...@gmail.com

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Jan 7, 2017, 7:51:50 AM1/7/17

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Hi everyone,

I've just started using MSstats and I'm pretty new to R in general. When using ProgenesistoMSstatsFormat() I get the following error:

Error in `colnames<-`(`*tmp*`, value = c("ProteinName", "PeptideSequence", :

'names' attribute [5] must be the same length as the vector [3]

I think this means that it's trying to assign 5 values to a vector with a length of 3 but I don't understand how to make it not do this and still have it work correctly.

Any ideas?

Cheers,

Venk.

Meena Choi

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Jan 17, 2017, 12:07:36 AM1/17/17

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Dear Venk,

I just posted about new release of MSstats. Could you try with new version? But, before using new version, please check 'Suggested workflow with Progenesis output for DDA' in user manual for v3.7.3, p 35, especially about output of Progenesis.

If you still have error message, please let us know.

Sincerely,

- Meena

vjmall...@gmail.com

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Feb 3, 2017, 10:30:25 AM2/3/17

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Hi Meena,

Sorry for the delayed reply. I'm getting a different error now:

> quant <- ProgenesistoMSstatsFormat(raw,annot)

Error in `$<-.data.frame`(`*tmp*`, "ModifiedSequence", value = character(0)) :

replacement has 0 rows, data has 144036

> traceback()

4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d",

"replacement has %d rows, data has %d"), N, nrows), domain = NA)

3: `$<-.data.frame`(`*tmp*`, "ModifiedSequence", value = character(0))

2: `$<-`(`*tmp*`, "ModifiedSequence", value = character(0))

1: ProgenesistoMSstatsFormat(raw, annot)

Thanks for all your hard work!

Cheers,

Venk.

P.S. Here's the top of my data if it's any help:

> raw[1:5,]

X X.1 X.2 X.3 X.4 X.5 X.6 X.7 X.8

1

2 # Retention time (min) Charge m/z Measured mass Mass error (u) Mass error (ppm) Score Sequence

3 15 47.9748166666667 2 655.3066223543 1308.59869177484 0.00249177484010943 1.90415870083486 7.6 EKEQVTEPAAK

4 696 47.9560833333333 1 1309.6061186981 1308.59884223122 0.00264223122167095 2.01913410849806 --- EKEQVTEPAAK

5 120 41.4649 2 917.464976846117 1832.91540075847 0.00380075847351691 2.07361799309738 7.79 NAAGAISKPSDSTGPITAK

X.9 X.10 X.11 X.12

1

2 Modifications Accession Description Use in quantitation

3 [6] Phospho (ST) 2::A0A0A0MTS7_HUMAN Titin OS=Homo sapiens GN=TTN PE=1 SV=1 False

4 [6] Phospho (ST) 2::A0A0A0MTS7_HUMAN Titin OS=Homo sapiens GN=TTN PE=1 SV=1 False

5 [8] Oxidation (K)|[9] Oxidation (P)|[11] Oxidation (D) 2::A0A0A0MTS7_HUMAN Titin OS=Homo sapiens GN=TTN PE=1 SV=1 False

X.13 X.14 X.15 X.16 X.17 Normalized.abundance X.18

1 EP 2kPa

2 Max fold change Highest mean condition Lowest mean condition Anova Maximum CV 20161008_VM2 20161008_VM4

3 2.36912283474593 LP 25kPa EP 25kPa 0.0243463279839192 57.5212699457085 395182125.240772 313867202.292051

4 6.02874578069378 LP 25kPa EP 2kPa 0.0112550252099755 67.9208547661788 28409501.0497393 19018425.9318489

5 1.85390116156622 LP 2kPa EP 2kPa 0.456975274047897 54.3177538790076 114373951.39887 109364446.603405

X.19 X.20 X.21 X.22 X.23 X.24 X.25 X.26

1 EP 25kPa LP 2kPa

2 20161008_VM9 20161008_VM13 20161008_VM3 20161008_VM7 20161008_VM14 20161008_VM16 20161008_VM1 20161008_VM5

3 459413632.014075 175041787.48833 295169637.101682 291875424.359262 202702052.030879 315389660.714875 664372126.634925 511644474.723947

4 29885062.4731013 984198.808521206 23112717.4380451 42269553.7562955 31126770.515835 46688015.6912473 99308550.5081195 89841500.8757293

5 135599548.915233 41847694.160632 75251398.9651892 147887092.316231 97879662.3572932 249599343.430278 165561282.242826 224098079.997074

X.27 X.28 X.29 X.30 X.31 X.32 Raw.abundance X.33

1 LP 25kPa EP 2kPa

2 20161008_VM6 20161008_VM12 20161008_VM8 20161008_VM10 20161008_VM11 20161008_VM15 20161008_VM2 20161008_VM4

3 620691297.955953 481990003.060783 1184000492.90288 462804988.451781 645646198.05811 325753087.87777 246255497.380567 173604899.050143

4 85111580.4600158 70680657.913681 157260735.656286 96120587.8639809 154871816.471186 63780703.3905637 17703219.2614351 10519391.2899476

5 250185216.920219 103913946.838335 47307950.6530014 226511214.241421 157081447.281561 220510305.264351 71271478.3644362 60491200.0158344

X.34 X.35 X.36 X.37 X.38 X.39 X.40 X.41

1 EP 25kPa LP 2kPa

2 20161008_VM9 20161008_VM13 20161008_VM3 20161008_VM7 20161008_VM14 20161008_VM16 20161008_VM1 20161008_VM5

3 177841142.357756 23894440.8282541 261751061.939397 402320616.528033 291229575.457181 443661081.423675 611831638.765855 645021253.889299

4 11568645.9418914 134350.091660347 20495937.1604656 58264285.0624709 44720988.6227437 65676393.7161221 91454940.3338113 113261611.155726

5 52491212.7151304 5712505.94654011 66731570.9873576 203847330.715893 140627350.481209 351113331.926971 152468212.572179 282516535.787641

X.42 X.43 X.44

1 LP 25kPa

2 20161008_VM6 20161008_VM12 20161008_VM8

3 620691297.955953 418789454.955784 809419433.136839

4 85111580.4600158 61412713.9891194 107508312.937869

5 250185216.920219 90288314.8662369 32341181.3001322

> annot

Run Condition BioReplicate

1 20161008_VM2 EP2kPa 312

2 20161008_VM4 EP2kPa 191

3 20161008_VM9 EP2kPa 112

4 20161008_VM13 EP2kPa 309

5 20161008_VM3 EP25kPa 112

6 20161008_VM7 EP25kPa 191

7 20161008_VM14 EP25kPa 312

8 20161008_VM16 EP25kPa 309

9 20161008_VM1 LP2kPa 112

10 20161008_VM5 LP2kPa 312

11 20161008_VM6 LP2kPa 191

12 20161008_VM12 LP2kPa 309

13 20161008_VM8 LP25kPa 312

14 20161008_VM10 LP25kPa 309

15 20161008_VM11 LP25kPa 191

16 20161008_VM15 LP25kPa 112

Canan Has

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Jul 13, 2017, 7:07:05 AM7/13/17

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Hello,

Did you find out the reason of this error? Because currently I also get the same error for my progenesis file.

Could you share the reason/solution?

Thanks in advance.

Best,
Canan

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